Depending on choices during the Culture Festival Breather Episode, the Protagonist can also show an interest in cross-dressing and has the option of willingly taking a seat on the girl's side of the table during the Group Date Cafe so that he can flirt with Yosuke or Kanji.
There are also a number of (presumably) Celibate Hero options such as stating a lack of interest in the Miss Yasogami beauty pageant and telling Yosuke that you have no romantic interest in either Chie or Yukiko. Picking such options usually leads one of the party members to make a not-so-subtle crack about the Protagonist's sexuality.
Though in episode 7 of the anime, he's just as freaked out by the... atmosphere of the bathhouse level as Yosuke is.
And then in episode 12, it's Yousuke who pulls him out of an Heroic BSOD during the fight against Shadow Mitsuo, in a scene that drips with Ho Yay. Not helped by how they start referring to each other in a First Name Basis.
Yosuke has more than a few moments with the Protagonist. "I'll invite Daisuke; don't want to look like we're dating." "You look like you're good with your hands—uh, never mind." "If I had to choose, I'd choose you! You're so handsome and reliable! Tee-hee!"
The entire Magician Rank 9 scene. It has the wonderfully ambiguous "I have family and friends... and you," as well as "You're special to me." Not to mention the Rank 8 scene. If you choose "You were just upset" in Rank 7, you will get the option to hug him (and I mean the around-the-waist kind) after the rank goes up.
Not to mention the Rank 5 scene where he awkwardly asks whether you keep the goods under your futon and if you've ever invited a girl into your room. If you answer the latter in the negative, Yosuke says "I guess you're more of a man's man than I thought!" and the narrator informs you that "Yosuke looks happy..."
Chie's and Yukiko's friendship is popularly interpreted as romantic. The conversation on Saki's appearance on the Midnight Channel ("My soulmate is a girl?"). Who was Yukiko's Prince? Chie! It helps that their respective shadows actually talked about their dependency on one another.
And the anime takes it Up to Eleven, very much so.
Also, Teddie is totally gay for you. Seriously. Talk to him before you leave Inaba and you'll get a conversation in which Teddie offers to take off his outfit for you.The suggestion is quickly declinedby Yosuke.
If you don't max out Yosuke's Social Link, you get this conversation instead. It is not any less homoerotic.