Depends on what you mean "favorite" at:
Favorite
loving relationship:
- Kaoru Hanabishi and Aoi Sakuraba from Ai Yori Aoshi - Aoi's unconditional love and devotion combined with Kaoru's obvious feelings and determination make them a wonderful couple. No silly dancing around their feelings (like Keiichi in AMG for example), either, they both express their love to each other in no uncertain terms.
Favorite
comedy relationship:
- Sosuke Sagara and Kaname Chidori from Full Metal Panic!- Sosuke is just the prefect straight-man for Kaname's tsundere act and his random actions of thoughtless violence around school just add to the humor. Even their "almost" confessions are funny.