Misplaced Affections
Digimon
Yamato and Mimi
Taichi and Sora
Takeru and Hikari
Kouji and Izumi
Ken and Miyako
Ryo and Rika
Naruto
Neji and Tenten
Shikamaru and Temari
Naruto and Hinata
Asuma and Kurenai
Flame of Recca
Tokiya and Miki
Raiha and Fuuko
Kurei and Neon
Recca and Yanagi
Hunter X Hunter
Hisoka and Machi
Card Captor Sakura
Touya and Nakuru
Syaoran and Sakura
Shaman King
Yoh and Anna
Ren and Jun (in a non-incest way, but a brother-sister dynamic)
Yu Yu Hakusho
Kurama and Botan
Yusuke and Keiko
Vision of Escaflowne
Allen and Millerna
Van and Hitomi
You're Under Arrest
Tokairin and Natsumi
Akazukin Chacha
Seravi and Dorothy
Miracle Girls
Noda and Tomomi
Kurachige and Mikage
Wedding Peach
Yousuke and Momoko
Yanagiba and Yuri
Sailor Moon
Haruka and Michiru
Mamoru and Usagi
Rurouni Kenshin
Kenshin and Kaoru
Sanosuke and Megumi
Neon Genesis Evangelion
Kaji and Misato
Gokudo-kun Manyuki
Gokudo and Rubette
Fushigi Yuugi
Nakago and Soi
Suboshi and Yui
Tamahome and Miaka
Hotohori and Nuriko (probably not yaoi per se)
Ouran High School Host Club
Hikaru and Kaoru (as twin brothers)
Rave Master
Musica and Reina
Haru and Elie
Gatekeepers
Shun and Ruriko
Teen Titans
Robin and Starfire
X-Men
Gambit and Rogue
Lance and Kitty (X-Men: Evolution)
Piotr and Kitty (X-Men)