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Some have pointed out that Gaeta and Baltar of the remade Battlestar Galactica (Gaeta especially) behave like a love affair gone sour in the third season. (And just what did Baltar whisper to Gaeta anyway?) It doesn't hurt that more than one of the actors involved in the show have explicitly stated they believe the character of Gaeta is gay.
Actually, this trooper saw some Gaeta->Baltar as early as season 1, "6 degrees of seperation," when Gaeta, of his own accord, re-scanned the disc 6 had given him, which showed Baltar blowing up Caprica's defence HQ, and proved it had been false.
The "Face of the Enemy" webisodes makes this canon, with Gaeta/Hoshi. According to Jane Espenson, Gaeta is bi and has mostly been in relationships with other men. Also, homophobia does not exist in the Battlestar universe, and so there is no concept of "coming out of the closet".
You can read Apollo/Helo Ho Yay into "Torn" and Apollo/Anders Ho Yay into "The Son Also Rises".
Surely this troper can't have been the only one to get some serious Lee/Lampkin vibes in late Season 3 and into Season 4. After being assigned to a position as bodyguard to Lampkin, an intensely unpopular man, it takes Lee less than one episode to form an almost obsessive emotional attachment to his charge; this, in turn, results in Lee's willing resignation of his entire career in favor of joining Lampkin in the task of legally defending the most hated human being in existence. Later, upon the realization that Lee is the best candidate for president of the Colonies and driven to despair by the killing of his beloved cat, Romo nearly kills Lee, believing that his assumption of the presidency would be a beacon of hope to an undeserving race. Lee reacts by making his first presidential act the acquisition of a dog for Lampkin, which then appears with or is mentioned by him in each of his later appearances. Aww.
Then there was canonical Gina/Cain and Caprica/D'Anna. The latter technically being Sister Sister Incest.
The possible relationship between Zarek and his former cellmate Meier was joked about by those on set, especially as the actor playing Meier had been in "Cruising" (1980).
In a deleted scene Head-Six comments to Baltar upon seeing Starbuck "If you sleep with this one, I'll join you." Unfortunately when this happens we only see Head-Six watching with disproval from the sidelines. Arrgh!
The Writer's Bible document shows that the plan was originally for Head Six to join in.
To call what goes on between Lee and Sam on the Algae Planet subtext is like saying Saul enjoys the occasional drink. It doesn't help that they're both sweaty and wearing muscle shirts. Word of God even pokes fun at this.
Speaking of Saul Tigh, it's pretty much canon that he and Bill Adama are the real love story of the series. Even his wife, Ellen, is rather ticked that Saul "loves" Bill more than her, and always has.
Search for "Brokeback Galactica".
That one will also get you Lee/Sam.
Also, Starbuck/Kat. Starbuck holds Kat to higher standards than any of her other students, and when it is revealed that Kat has been taking stims (something that Starbuck disapproves of), Starbuck is personally offended. Kat is also the only one who will consistently call Starbuck on her various hypocrisies, and in the episode "Scar," the two of them engage in a heated competition to kill the titular raider, with the prize being the right to drink out of Starbuck's cup. Later, Kat dies heroically, prompting Starbuck to tell her friends that when she dies, she wants her picture placed next to Kat's. And when Starbuck puts Kat's picture on the wall of memories, it is next to the word LOVE.
Several times in "Scar" and "The Passage" their faces were so close together this troper can't believe they didn't kiss.
Sam and Galen spend a lot of the fourth season giving each other meaningful looks. Now, granted that was largely due to them both being cylons, but still.
How did they spend the time on that ship heading from Earth to the Colonies? Sam/Tory/Galen threesome, anyone?