Listed (mostly) in order of preference for each generation. Gen 1 has a top 8 instead of a top 5, because I love soooo many pokemon from that gen:

Gen 1:
1) Kabutops
2) Aerodactlyl
3) Arbok
4) Charizard
5) Mewtwo
6) Charmeleon
7) Vaporeon
8) Rattata

Gen 2:
1) Houndoom
2) Quilava
3) Xatu
4) Ariados
5) Scizor

Gen 3:
1) Mightyena
2) Grovyle
3) Blaziken
4) Manectric
5) Absol

Gen 4:
1) Lucario
2) Riolu
3) Garchomp
4) Gallade
5) Luxray

Gen 5:
1) Haxorus
2) Krokorok
3) Liepard
4) Archeops
5) Serperior

Gen 6:
1) Greninja
2) Heliolisk
3) Noivern
4) Xerneas
5) Hawlucha

Much to my surprise, I actually still knew all their names, though I did have a lot of trouble with Gen 5, since I really didn't do much with Black and White.