I use a program called Ransen Scan (ransen.com) that automatically picks out the individual cards when I scan 9 at a time. It relies on contrast between the border of the item you are scanning and the background of the scanner lid to tell where the edges are. Sometimes it does a great job, but most of the time you still need to do a bit of trimming to get excess white or black off the image. Since the scanner lid is white, of I'm scanning cards with light borders, I just leave the scanner lid up, so it gives a dark background for contrast.
There used to be a great program called Instant Photo Scanner, that did a much better job, by a German company, but they abandoned the software, and now you can't even buy it. Some scanners come with software that can already pick out separate items on the scanner bed, but those seem to be few and far between.
I typicall scan everything at 600dpi, and then resize down to 1000 pixels on the longest side before posting. Oh, I use ACDSee for all of the rotating, cropping, resizing and whatnot.