I know this is a near impossible question as the different anime I can think of have literally hundreds, well it could be done but it would take a while to compare and contrast the sheer numbers of characters
Anyway the ones' that spring to mind
. Transformers (G1 I guess)
. Dragonball / Dragonball - Z
. Naruto
. One Piece
. Pokemon and whatever series it's morphed into now
Anime (aside from Dragonball) that seem to have been going on for all of eternity, that have been around longer than I have and may be around after I'm gone even xD
I'd say it's out of Naruto (it has got a dumpload of characters), Dragonball / DBZ and Transformers