I'll do Legendaries and non-Legendaries separately.
Non-Legendaries: 1. Alakazam with Gyarados not too far behind. 2. Scizor. Hands down. 3. Blaziken with Swampert close behind. 4. Weavile by a fair margin. 5. Haxorus with Volcarona occasionally rising above him depending on my mood.
Legendaries: 1. Mewtwo. Duh. 2. Lugia. 3. Rayquaza, but Groudon's cool too. Latios is also up there. 4. Uhh... Giratina? Maybe Heatran and Regigigas too... 5. My White 2 starter, Genesect.
This guy is actually fairly close to me, mentioning my favorites for 4/5 generations each both legendaries and non-legendaries.
Not changing this sig until The Undertaker vs. Chris Jericho happens on PPV (started October 4, 2009)