There seems to be plenty of this between Apollo and Starbuck as the original series progressed. It's especially evident in the second part of "War of the Gods" in which Apollo is 'killed' and Starbuck falls apart, losing his head and then collapsing in tears. Then he offers the Beings of Light his life in exchange for Apollo's and when Apollo is restored, Starbuck smiles through his tears. It's as if the Beings of Light saw something that Starbuck's offer wasn't even needed in the first place. Since then (and even before), the two warriors would risk their lives for each other.
Starbuck is even jealous of Apollo's prospective bride Serina who is set to replace the former much to the dismay of both men, though Serina would later succumb to Cartwright Curse. Then again, it may have been just about being replaced as Apollo's wigman. As if. Later comes a reunion scene between the two in which they embraced.
Starbuck:"Don't you know it's against regulations to hug a junior officer?"
Apollo:"Not if I mean it."
On top of it, Apollo would often tell Starbuck 'it's me, Apollo' whenever Starbuck doesn't want to say what bothers him or what he intends to do about it. It often works.
Apollo:"Hey. It's me, Apollo. Remember? We talk about things."
Some have pointed out that Gaeta and Baltar of the remade series (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".
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.
Take a look at the Season Two opener, "Scattered", Adama has been shot and Tigh flashes back repeatedly to the first time the two met.
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.
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?
Amanda's relationship with Sister Willow is somewhat interesting. One the one hand, she's an emotionally unstable woman relying on her religious offical for support. On the other hand, they seem to be really close. Also, said leader is both a)bisexual and b)polygamist. Who's to say her seven spouses wouldn't be willing to share? There's also a certain amount of this with Clarice and Lucy.
David Eick said in a commentary that the writers toyed with the idea of making Amanda/Clarice fully sexual but decided to go with deliberate Les Yay.