My favorites during the first generation were definitely Pidgeot and Articuno. I mainly used them (and Zapdos) to sweep the Elite four. I have long since given up using legendaries to beat them...>___>
Then in Gen 2, I was introduced to Typhlosion, and I loved it, and I have ever since. I even hacked in a Cyndaquil into my LeafGreen, in order to upload it onto my Diamond, then make an egg, all so I could have it as my starter for my playthrough of Platinum. XD
I don't really remember playing through Gen 3, (I had gotten an AR, and I hacked the heck out of my Sapphire. XD Then I lost my Sapphire and haven't played it since, so I have little recollection of a normal Sapphire playthrough) but I do believe that my favorites were Ninjask and Gardevoir.
Then Gen 4 came around, and I found out Electabuzz had an evolution, a pwnsome one, at that. SO I set out immediately to obtain one, and I am really glad I did. ^__^
So yeah, those are favorites. ^___^