Hah. This topic comes up all the time... I wasn't a big fan of the old official SR minis, so I've been using alternatives for years. I use a mixture of old VOID, Warhammer 40k, a few old SR miniatures, the occasional Dark Ages minis and other random crap for my games... basically any time I go to a gaming store I keep in mind what I need more of (opposition, mostly), and buy accordingly if something catches my eye.
Characters and Corps are easy, I've had problems finding good 'bulk' Yakuza and Gangers... and Trolls are always a tough find.
Other manufacturers/lines to look at: Chronoscope (by Reaper), Wargames Factory (if you like a LOT of assembly time), MERCS,
Hasslefree,
Heresy Miniatures, Infinity(awesome, but expensive)