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Anticlimax Boss: War's first phase is exactly what you would expect having seen Pestilence and Famine, with no summons but more aggressive attacks. His second form... is basically a quicker Lust but saddled with Gemini's poor running stamina, far too late in the game to be very intimidating for anyone with speed upgrades.
Mom's Heart will rarely pose a serious threat to anyone who is good enough to reach it.
When Wrath of the Lamb was first released, even Satan was this if you brought The Polaroid to the boss fight.
He has been been given more HP in version 1.15, making him a Damage Sponge Boss.
Awesome Music: The entire soundtrack by Danny Baranowsky.
He's pretty well-known for his awesome video-game music (as can be heard in Canabalt and Super Meat Boy).
Special mention goes to the battle themes: "Divine Combat", "Burning Ambush", "Thine Wrath...", "...Be Done", and "Enmity of the Dark Lord".
Best Boss Ever: Loki, an always-smiling demonic baby, is quite preferred over Monstro II as the boss of the fifth floor. They even call him "Mr. Cool" in the credits.
Though not so in the TRUE Brutal Bonus Level, which can quite frequently feature any Harbinger (even Death is normally fought only two levels ago) in a room far more restrictive than the one you normally fight them in.
Pride's diagonal tentacle attack probably won't hit you if you're firing at him with your tears, and his bombs are for the most part easy to avoid. Compared to every other Sin, Pride is the least threatening.
Breather Level: Even during the Brutal Bonus Level, there will occasionally be rooms with only a fly or a pair of helpless grubs, which still recharge your special item and have a chance to drop items. There will also always be some empty rooms, and it's possible to spend quite a long time in the arcade with virtually no chance of death.
Complete Monster: Isaac's mom, for unquestioningly obeying God when He told her to murder her own son. Curiously, God Himself is not even a villain, even if He is Old Testament. This is in defiance of other anti-fundamentalist fiction.
Leapers. Just... Leapers. Their erratic jumping makes them hard to hit consistently, they can jump to any part of the screen with little warning, and when there's four of them, the screen tends to be filled with bullet spam from repeated jumps. A real pain to deal with.
Mr. Maws. They swing their head at the player, which can be very hard to dodge, and upon death they leave shooting heads (and sometimes slow-moving bodies) behind which can be a problem of their own. They can be the utter bane of people going for No-Hit runs, because there's one room configuration that they are practically impossible to dodge as you enter.
Knights with an Isaac's face at the back of their heads charge the player when they see him.
Eyes, especially when they're not located in the center. These are likely to hit the player. The bloodstream versions are even more dangerous (especially without having a weapon to shoot over rocks), as bloodstreams last longer than Eye Beams and they're often situated between rocks, making it hard to hit them.
Clotties, when in groups or in certain room layouts. They move around haphazardly, fire in all four cardinal directions at once (which forces you to either put yourself in danger to hit them every time or use unreliable diagonal shooting, which may not always be viable in certain layouts), and do so at completely random intervals (i.e. not guaranteeing you'll even have enough time to try to hit them) with next to no warning. Even worse are the white "Alternate" varieties that do 8-way shotsm making even diagonal shooting dangerous.
Every enemy can become this in The Womb and beyond, since all damage taken there will be one whole heart of damage instead of half a heart.
WOTL's new Spider enemy (not the leaping spiders) are this. They move VERY fast, like to pin you in, and are EXTREMELY ERRATIC.
Not the leaping spiders? They're even worse!
Game Breaker: Despite the impact of Luck on survival, combinations of certain items can become this.
Special mention goes to a fully formed Meatboy — who is invincible, blocks shots, and will hunt down enemies in the room and kill them with a cheery smile.
Though he can only be obtained in time for the last level; not that level 3 Meat Boy isn't pretty useful already.
Battery + My Little Unicorn. Allows the player to make short work of problem rooms and still be prepared for future conflicts.
The Battery, in general, is pretty useful. It causes items to regenerate at a fixed rate while in combat instead of just at a per-item rate after combat. It is limited per room, but resets its counter when the item is used and can in fact guarantee one use per room of any item with enough patience. That includes items that would normally grant soul hearts, pills, tarot cards, Super Star invincibility, level skips, and random items once every six rooms.
The Ladder (and later/rarer items which allow proper flight) is surprisingly useful. Most enemies utterly forget about you if you stand on a pit, even if it's a 1x1 square. This makes fighting the Knights a LOT easier.
Better yet, flight plus the Ouija board (which lets you shoot through walls). You could theoretically beat some bosses (like Chad) and many other rooms by hovering over a rock/pit and taping down the fire button. Projectiles and most enemies will not be able to touch you if floating over an obstacle, but yours will still hit them.
Mom's Bra or the Book of Shadows can basically win a room by themselves or put the serious hurt on a boss during their duration and can be used once every three rooms. The Book of Shadows gets a special mention because if you have Poison Touch from The Virus to go with it, you've essentially got My Little Unicorn with a faster recharge rate. Mom's Bra (or Mom's Contacts, though not as reliably) does protect you from collision damage, only with it the bosses won't be running away while you drain two thirds of their lifebar with The Virus.
If you've mastered fighting Wrath's ability to kick bombs, Dr. Fetus becomes this, giving you the ability to shoot infinite bombs.
Master nothing. Add Bobby-Bomb (homing bombs), and who needs aiming? Additional items like Ouija Board (bombs pass through walls) and Mr. Mega (HUGE bomb) makes most of the game a breeze.
If you know how to use it, then the base skill can become this. If you can avoid enemies and get them hit by the bombs, then you can kill every enemy in the game with basic bombs.
The nail. When used, it gives a spirit heart, increases damage, and lets player walk over rocks among with the other benefits. This was even more broken in earlier versions, where it gave two spirit hearts.
Steam Sale (everything in shops half off) + dollar (maximized cash) = shops being very useful.
If you happen to have a second copy of Steam Sale (which makes all shop items free of charge in Rebirth, or 75% off in Repentance) as well as Restock (which automatically restocks shop items upon purchase without using the restock box), you can rapidly purchase a huge stock of items with little to no budget.
After the Halloween update, Brimstone. It replaces your previous attack with an extremely powerful and wide beam which can fire through obstacles but must be charged beforehand... except that you can charge your next shot while the current one is still firing, thus rendering its only downside moot.
Originally, if you combined it with the Chocolate Milk, the charge time for the beam was removed. This allowed you to spam beams as much as you wanted, making most enemies and bosses go down in a couple of seconds. However, a later patch severely changed the behavior of said two powerups, turning the two items from a game-breaking combo to a game breaker of a different kind.
Mom's Knife + Mom's Contact. Mom's knife does rapid high-powered damage. Mom's contact has a chance of turning the target to stone per hit. Rapid hit + stone chance = stone enemy. Now, keep in mind Isaac can then just walk up to said immobile enemy with the knife which will continue to do rapid damage plus turn them back to stone — so only enemies with backup will survive once that first stone hit kicks in.
Mom's Bottle of Pills + PHD. One pill every six rooms, with PHD making most of the bad side effects from them non-existant. You might get the occasional neutral pill (such as Bombs Are Key) here and there, but it really helps if you want to increase your stats by a large amount in a very short amount of time. You can even use it with the Battery (plus the 9-Volt to speed up your stat-increasing even more!
The Prayer Card is the Game Breaker to end all Game Breakers. Once per six rooms, it allows you to create half of a Prayer/Eternal Heart. If you finish the stage with one of these, or manage to obtain a second one, you get a full heart container. To put it simply, if you're skilled, it lets you pull entirely new heart containers straight out of your ass, for free, every twelve rooms. It gets even more hideously broken if you manage to get the Battery with it, giving you the opportunity to give you a new heart container every two rooms. Naturally, this tends to make you able to completely buy out the Devil Room shops, making you an unstoppable force with insane power and health that doesn't even fit on the screen.
The same could be said of ALL the new WOTL items, as they are all horribly horribly overpowered and gamebreaking.
Technology 2 (which shoots a laser that is weak as all hell but hits constantly) will pretty much guarantee victory if combined with Mom's Contacts (which give your shots a chance to freeze enemies) or The Mulligan (which gives you a chance to spawn a kamikaze attack fly whenever you shoot an enemy).
Knights are hard to hit since they're invulnerable in the front.
Hosts take cover and shoot 3-way shots. Sometimes weird maneuvers must be taken for them to show up. There is a red host variation which cannot take cover, but it shoots a 5-way spreadshot and fires more often.
Just mention Greed to anyone who's played this a few times and watch their blood boil. It's not just the fact that he's very hard to fight without being hit once (His attacks are completely random and have no tell whatsoever), but his appearance results in you losing the shop or secret room of that level. This can be annoying at best (meaning you've lost a key or bomb to get in for nothing), or utterly fatal (You SO needed that shop for health...). The exception is when not having enough money, as Greed drops a lot of coins.
The green variation of The Duke of Flies when not having any bombs or piercing shots. The Duke spawns Moters which can be dangerous if shot and it's hard to get a hit on him.
After the Halloween Update, the Mr. Boom item's recharge bar got permanently stuck on full charge. That equals to an infinite supply of super-bombs! This one was fixed in the bugfix that quickly followed the Halloween update.
There was a bug where ??? gained complete invincibility when he took a Full Health Pill. This invincibility would last until he picked up an item that would increase the maximum health of a normal character. It even counted for No Damage achievements. Eventually it was patched out.
As explained above, the Brimstone + Chocolate Milk combo was originally this, allowing you to spam blood beams all across the room for no charge delay whatsoever. However, this was quickly fixed for being too overpowered, and the resulting combo produced from it is now... less than satisfactory.
Defeating the Headless Horseman will sometimes unlock Little Chad and the connected achievement, even if you haven't cleared the Caves enough times to even unlock Chad himself.
On the less spectacular but more exploitable end of the scale, if you use the Temperance card to create a blood donation machine right next to one that was already there, you can use the mercy invincibility from touching one to activate the other without taking damage, doubling the rate of payout per heart. This could be extended even further if you find multiple Temperance cards on one level.
Wrath's bombs are treated as player bombs in order to make them pushable. This means that certain powerups which alter player bombs also affect his. Such as the Bobby Bomb powerup, which makes your bombs move towards the nearest enemy. The result is a hilarious easy win.
Before it was patched, using Lemon Mishap after defeating a boss and leaving the room through the door, re-entering the room would allow you to fight him again, earning you an extra item.
Before it was patched, the final boss fight against Isaac himself bugged out and had no music at all. This made it way more dramatic than the standard "Dark World Boss" theme.
Wrath of the Lamb had, and may still have a glitch where secret items don't need to be unlocked to be found.
It was possible to enter and exit Challenge Rooms at any time as long as your character could fly. In addition to allowing a player to enter Challenge Rooms without full health, it also allowed players to pick up the item in the room and then leave without fighting any enemies. This glitch was around since the game came out, to the point where it may have become an Ascended Glitch. However the expansion Wrath of the Lamb made the glitch even more game breaking by including more items that gave flight, as well as advanced Challenge Rooms that always gave a major item. The second update to Wrath of the Lamb removed this bug entirely.
Internet Backdraft: When the game was barred from release on the Nintendo eShop due to the religious content, all hell broke loose.
That One Boss: Even though the game's only been out for a short time, Gurdy's already gotten a reputation as this. It may be subjective, because boss difficulty varies depending on items obtained and if the boss is in its normal form or one of its alternate colors. "Default Gurdy" also has a simple pattern which once learned turns him into a Breather Boss. (Stick to a lower right/left 'corner' either below or next to him. Whenever the face ducks in, move across the corner; Gurdy can only shoot in 3 directions and that simple action puts you out of harm's way. Alternately, standing directly behind Gurdy is even easier, as he can't shoot in that direction, and his summons either can't hit you, due to being out of range, or are just simple flies that quickly moving left and right to hit will take down almost instantly after they spawn). Some alternative forms of Gurdy, however, never fire but instead attempt to swarm Issac with summons.
In WOTL, The new Widow boss is becoming this at an even faster rate, and it was just released yesterday at the time of this edit! They spawn demonic spiders, jump around like Monstro, AND spawn enemy that in turn spawn more demonic spiders, And there's a variation of this which spawns even MORE spiders, double spiders, and hopper spiders! Also it's a first floor boss. HAVE FUN.
It has been thankfully weakened in version 1.15.
The Bloat, a posthumous version of the Peep, is significantly harder and annoying than its living counterpart. It leaves a puddle of red creep whenever it jumps and lands to the ground, fires a Brimstone beam when you stand at the side or under it, fires eight projectiles in all direction, and you have to dodge all of the aforementioned attacks while dodging both of its eyeballs, which flies diagonally. The Bloat is infamously difficult to the point it has a Subreddit dedicated to ranting about it.
Urban Legend of Zelda: There are rumors floating around that beating the game five times with ??? unlocks Moses, who can turn enemies into money. No such character exists.