10. Finding the journals in the Pokemon Mansion in Cinnabar Island RBY/FRLG
9. The Fullmoon Island sidequest in DPP
8. The Trick House in RSE
7. Finding Articuno in HGSS
6. Locating Mewtwo in HGSS
5. The Abandoned Ship in RSE
4. The post-game sidequest in the Relic Castle in BW
3. Finding Lugia/Ho-Oh in the Whirl Islands/Bell Tower in GSC/HGSS (I can't remember exactly if this is technically a side quest or not)
2. The Regis in RSE
1. The Ruins of Alph in GSC/HGSS
How about yours?
Remember, Side-Quests refer to anything that is optional, from finding Legendary Pokemon that are not required by the plot to find (as in, not encounters with legendaries that are part of the plot, but the encounters that you aren't "required" to do) to doing optional tasks with NPC's to even the Pokemon Contests.