These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
"I Will Sodding Twat You", a song sung between Ed and Russell that's a parody of Queen's "We Will Rock You".
Ho Yay: Hughes and Mustang have some very... interesting interactions with each other and other characters. Made stranger when you consider their canoncharacterizations.
"Hey. Hey, Roy. Roooy~!"
"What is it, Maaaaaaes~?"
"I'm not wearing any paaaaants~"
"And I'm happy to see youuuu~" [Roy hangs up]
Aaaaand as of episode 11 Hughes is effectively shipping Roy and Ed. Mustang also threatens Ed with telling all of Central that Ed has a "massive man-crush on his tight ass" (at least, according to Riza) and it's suggested throughout the episode that people are already whispering rumors about them. Mustang lampshades the playing-to-the-shippers by telling Hughes "don't be so Tumblr!"
In the same episode, Roy says he wants to make "multicolored G-strings" a new part of the military uniform, and refuses to say anything when Havoc asks if it's "only for the women."
It's hard to hear over what Ed and Roy are saying, but one of the rules Hughes lists off before the Flame vs. Fullmetal battle is "Homoerotic interaction is not only allowed, but encouraged!"
Barry the Chopper shouts "I'm so hard right now" while trying to chop up Ed.
Ed asking Russell to suck his dick. Granted, it's an exaggeration of an actual line from the dub with some weird implications that way (where Ed asks Russell to "get on [his] knees").
Iron Woobie: Al, even moreso than in standard canon. His problems began even before he lost his body thanks to living with Trish and Edward, and now he's the Only Sane Man. Really, being a living suit of armor seems almost incidental by comparison.
Memetic Mutation: Tumblr's had a lot of fun with Belsio and his lemons fixation.