Here's a short list:
- Chloe (Smallville) - shipped with Clark
- Faith (Buffy) - shipped with either or both Winchesters (Supernatural)
- Rogue - shipped with Wolverine (X-Men - movie) or Cyclops (X-Men Evolution)
- Edmund (Chronicles of Narnia) - shipped with Peter
- Draco (HP) - shipped with Harry
ETA:
- Heero/Duo (Gundam Wing - 1x2) - closer to Duo
- Kanda/Allen (D. Gray-man) - closer to Allen
- Roy/Edward (FullMetal Alchemist) - closer to Ed
- Sasuke/Naruto - closer to Naruto
- Harry/Draco - closer to Draco
- Clark/Chloe - closer to Chloe