Charley, I envy your ownership of a Super Coolscan! They are THE best film scanner, at least at consumer level.

I can only speak from experience of using a good flatbed scanner (Epson 3170) myself. Colour negatives (eg Kodacolor) are always a problem with any scanner because of the orange mask which you can see when you look at negs. The density and hue of this mask varies according to the make of film. The "color negative" setting on Epson Scan software does quite a good job with Kodacolor negs, but the resultant scan always needs tweaking in Picasa, Photoshop or whatever.

A friend tells me that there is a known problem scanning some Kodachrome slides with a Nikon Coolscan - if you use Digital ICE to get rid of the dust etc on the slides, it doesn't work too well. This is something to do with the way the Kodachrome process uses a sort of dye sandwich, very different from Ektachrome, Fujichrome etc.

There's LOADS of stuff on the Web about scanning negs & slides and I'm afraid some of it does my head in! "The Kodachrome Project" is a good site, it's a sort of memorial to Kodachrome but with a lot of very good advice.   

Oh dear, sorry not much about APS there, I have to confess I hate the stuff, Kodak's last attempt to foist