Yaoi:
Seigaku (the name of the school):
Tezuka/Fuji
Tezuka/Fuji/Ryouma
Oishi/Eiji
Inui/Kaidoh
Momo/Kaidou
Momo/Ryouma
Hyoutei:
Atobe/Jirou
Oshitari/Gakuto
Shishido/Choutarou
Rikkaidai:
Sanada/Yukimura
Sanada/Yukimura/Kirihara
Jackal/Marui
Niou/Yagyuu
Fudomine:
Tachibana/Shinji
Tachibana/Kamio
Kamio/Shinji
Ishida/Sakurai
Yamabuki:
Akutsu/Dan
St. Rudolf:
Mizuki/Yuuta
Mixed schools:
OT5 = Tezuka/Sanada/Atobe/Fuji/Ryouma (Don't ask. It's not worth it. )
Saeki/Fuji
Fuji/Yuuta
(All of those are fairly standard. The next ones aren't standard but popular)
Atobe/Tezuka
Atobe/Fuji
Tezuka/Sanada
There's more, but that's a good start. PoT is hard to categorize cause there's SO MANY characters and so many threesome/group fics of specific pairings that they're either standard or almost so. Good luck. I'm happy to answer any questions, but other people might have some other ideas as to what's popular or standard.