Top five:
1. Noveria - gave the Mass Effect universe the most depth in that game. It really fleshed out the inter-glactic feel to the game, other than the Citadel
2.Ilos - Epic momentum and suspense propelling you through the Conduit. Oh, and Vigil is awesome

3. Lair of the Shadow Broker - Seeing Liara fully settle into her character was pretty sweet, the combat was incredibly fun, the banter was priceless, so many little details like the billboard of Blasto, etc. etc. I probably replay this mission the most.
4. Garrus Recruitment - very heartwarming reunion, definitely the best one in the game.
5. Thane's Recruitment and Loyalty Missions - Best Bw character, hands down.
Honorable mentions: Project Overlord, Arrival and Tali's Loyalty Mission
Worst:
1. An obscure side mission in ME1 where you are on a ship with Rachni, and there is a time limit. I HATE that mission D:
2. Horizon, for inexcusable actions of Kaidan (or character assassination of, take your pick) and the husks/scions and praetorian.
3. Acquire the Reaper IFF (damn husks, and scions)
4. Disabled Collector's Vessel
5. Noveria's boss fight (I love Mirina Sirtis' voice, but c'mon, battle's more glitched than DA2 ever was!)