Gen 1: Bulbasaur, Charmander, Squirtle, 10-12, Pidgey, Rattata, Raticate, 29-33, Vulpix, Paras, Parasect, Psyduck, Bellsprout, Farfetch'd, Magnemite, Magneton, Shellder, 92-94, Onix, Cubone, Tangela, Kangaskhan, Horsea, Magikarp, Lapras, Vaporeon (sometimes), Porygon, Omanyte, Articuno, 147-149, Mew
I have no idea if all of those were in Pokedex order, I'm going by memory.
Gen 2: Here's where it all comes crashing down, memory wise... Chikorita, Cyndaquil, Totodile, Sentret, Flaaffy, Wobbuffet, Lanturn, Unown, Girafarig, Sneasel, Miltank. Corsola and Shuckle are cute, but I wouldn't call 'em faves.
Gen 3: Treecko, Torchic, Mudkip, Illumise, Ralts, Kirlia, Gardevoir (sometimes), Sableye, Mawile, Trapinch, Vibrava, Flygon, Milotic, Latias, Latios
Gen 4: N/A, but at least I know who Buneary is, so Buneary by default.
Gen 5: N/A, except that I know about Golurk and it seems like a cool concept. Also, Gothorita or whoever for being "Dark Kirlia" or whatever.
Gen 6: N/A
I've taken notice that most of my favorites are female or feminine, unevolved or cute. Can't say I'm surprised at all, it really does come back to my preference for female characters in series, unless there aren't/are barely any (like Kirby).