Personally, my favorite Too Short period is the '93-'95 era, but I might be biased because GET IN WHERE YOU FIT IN was one of the first albums that got me acquainted w/ the Bay as a hot area for new Street Rap music back in the early '90s (at that time, I was bumpin' mainly South Central L.A. stuff, old school New York Rap from the late '80s and some of the better '90s East Coast Rap). That whole period where Short was working with Ant Banks, Spice 1, Pooh Man (until they had their feud), Goldie, Shorty B, Pee Wee and whoever else was the height of that whole "clean-sounding but still street" era of West Coast Rap music in general (although guys like Khayree, T.C. and the early JT-produced Get Low CDs took the same clean style and added their own touches, which was cool).
As far as his more recent stuff, I personally like WHAT'S MY FAVORITE WORD? and MARRIED TO THE GAME (even if WORD does sound Southern production-wise), but I couldn't really get into his '99-'01 period (CAN'T STAY AWAY, YOU NASTY, CHASE THE CAT). Just my opinion, though.
PEACE!