Alright, IMO, for 2D fighters, Street Fighter and King of Fighters are both equal as the best fighters of that particular genre. followed by series like AOF, FF, Gaoru and other SNK titles, Capcom's only real fighter has been SF IMO, Final Fights been great too, but thats another genre entirely.
for 3D, Namco produced my two favourites in the Tekken series, and the Soul Calibur/Soul Blade series, both are equal to me in terms of which is the best, followed closely by DOA. Capcom's project justice was nice for a litle while, but without it's connection to SFer, it fades into obscurity.