Supernatural - Dean and Sam, Dean and Castiel or a threesome between these men works too!
Doctor Who - Rose and the Doctor
Bones- Bones and Booth
Stargate SG1 - Daniel Jackson and Samantha Carter or Jack O'Neill and Samantha Carter
X Files - Mulder and Scully
Gundam Wing - Heero Yuy and Duo Maxwell
Hellsing - Seras and Pip
Kyo Kara Maoh - Yuri and Wolfram
Saiyuki - Hakkai and Gojyo
More to come later...