Hi Jamie,
I've been using my coolscan 9000 for a few years now. I use nikon's software for my scans.
For b/w film:
scan as gray scale positive
16 bit
no ICE, no sharpening. No multi sampling.
Another important tip is to mask your negatives, when placing them in the glass carrier. For the longest time I would get dark bands across the top and bottom of my 6x6 frames. Its caused by stray light hitting the negs - I made some small strips out of black paper that I place in between frames, and it takes care of the problem. I usually don't see this problem with slide film, but it does happen, so I'd recommend always using the masks.
For slides, I scan as rgb transparency, 16 bit, no sharpening, and no ICE. No multi sampling.
My standard print size is 10.5" x 10.5" so I scan at 2500, which gives me plenty of resolution. The biggest I've printed from 6x6 negs is 15" x 15" and if I remember correctly I scanned my neg at 3500 and the resulting print was tack sharp.
Hope this helps
Mike