Pre-rewrite North. For a whining Butt MonkeyOC Stand In with little impact on the plot, he's strangely popular with the readers.
Sheila is fairly popular thanks to being one of the few characters to be a genuinely good person and a total badass at the same time. Her wholesome relationship with Lopez doesn't hurt.
Sister. She only appears sparingly outside of flashbacks, but much like in canon she's universally beloved by the readers. Even the author has expressed regret about her not showing up more, since there's no logical way to fit her into the plot.
Harsher in Hindsight: Grif once references the high rate of injuries and speculates that Simmons will be next because he hasn't been hurt yet. Not long afterwards, Simmons is disembowled and Killed Off for Real. In the same vein, Grif says that Sister can't call her future son Simmons because you can only name children after dead guys.
Holy Shit Quotient: The later flashback chapters tend to veer upwards with the HSQ. As did part 109.
Iron Woobie: Donut. He goes through a lot of shit in the prison, including being a magnet for vicious attacks that leave him hospitalized for 35 chapters. But he never, ever gives up and just continues toughing it out. To put it in his own words, 'If I gave up whenever things got difficult, then I would have kicked the bucket when my roommate attacked me.'
Jerkass Woobie: Wash. There's no denying that the guy is a complete asshole, and half-psychotic to boot. But factor in the backstory and it's easy to see why. Whether he's more Jerkass or Woobie depends on the chapter.
Mind Game Ship: Doc and O'Malley, which is little more than O'Malley constantly playing around with him and threatening to hurt other people if Doc stays away.
Much to do with Tucker being separated from Junior is somewhat tearjerking, but the worst is when Tucker gets blinded and realises that he'll never be able to see Junior's pictures again or see Junior grow up.
Simmons' death. As well as Grif's grief over it.
Maine's death in the rewrite. He actually did consider Donut a friend and was only trying to knock him out so he could help Epsilon break Church out of prison, but Donut mistook it for a murder attempt and brutally killed him in self-defense.
The Woobie: Several characters could qualify. Donut is the Iron variety, as mentioned above. Doc is another example, especially considering O'Malley's constant hounding of him. Caboose could qualify, but considering how violent and twisted Caboose is in this, his woobie status is more questionable.