Question

One of the uke favorites for me has to be Ao from Yume Musubi, Koi Musubi!!! XD

Seme: Iason Mink (Ai no Kusabi), Doumeki (Saezuru), Asami (Finder)
Uke: Yashiro (Saezuru), Shima (Doushitemo), Riki (Ai no Kusabi)
but I have many, many more

Ukes (in no particular order):

Asakura, the shop proprietor, from Metro Dog, because he sees the beauty in broken things and people alike, then loves and repairs them.

Serizawa, the bookstore employee, in Café Latte Rhapsody because as soon as he sees the gentle person Keita is, he drops his prejudiced ideas about his appearance and, even stakes his job on this, sticking up for Keita when he is unfairly accused of shoplifting.

Kashiwaya, from Hatsuai, because he's a totally fearless artsy freak, both hilarious and loveable and I wish I had some friends like him.

Semes (again, in no particular order):

En Ma Daiou from Jigoku Meguri, because he never loses his humanity in spite of his awesome supernatural powers, and because he persistently loves Takamura for all his flaws, and takes on his karma even when he breaks the laws of hell.

Stray cat, Fuji, from Sentimental Garden Lover, because he's so sweet and protective.

Takitani, from Solo Sex, because he is so caring toward his younger brother when their parents are accidentally killed, and because he totally doesn't care if his friends aren't cool.

Uke =
1: Nemu ( Hidoku Shinaide )
2: YakushiJi (Leopard Hakusho)
3:Eta (Kamisama no ude no Naka)


Seme =
1: Maya (Hidoku shainde)
2: Lancelot (Kamisama no ude no Naka)
3: Fumi (Elektel Delusion )

<333333333333

uke:
Ayase (okane ga nai)
aki (honto yajuu)
levi ( from the dj of attack on titans )

seme:
sebastian ( dj of black butler )
tomoharu (honto yajuu)
fuuta (kawaii akuma )

they are all so so hot.. yeah! <3 <3 <3 ^_^

Naruto Uzumaki(Seme)Sasuke Uchiha(Uke), both from the Naruto series.
I know you said to pick three, but I just adore these to characters. They are my #1 in my heart.

I wish I could all these answers because I want to read these manga now.