When I first built this site, digital photography meant scanning my slides and using Photoshop. The dedicated film scanner ruled and flatbeds were seen as a general purpose tool. A lot has changed in the last few years. We now have 35mm cameras and other digital backs that surpass medium format film quality, and you'd be hard pressed to find any new film scanners since 2005 as many photographers have now moved to an entirely digital workflow.
Nevertheless, here are some tips from my slide scanning days using a Polaroid Sprintscan 4000.
Calibration
Apple's integrated color management makes this Windows user green with envy. Along with your monitor, you'll need to calibrate your scanner to achieve good results. Mine came with an IT-8 target so a custom profile was one scan and five minutes away. Choose the output space to match how you configured your editing software - in my case it's Adobe 1998.
Dust and Noise
The thing I spend the most time on after a scan is cleaning up dust and noise. I finally got smart and began handling my slides more carefully (cotton gloves) and using a static brush to remove the majority of dust spots. I don't think you can eliminate the dust, but you certainly can reduce it.
If you scanner is so equipped, you can take advantage of the built-in Noise reduction but don't overdue it as you'll lose sharpness.
Transparency vs. Negatives
For me, I found scanning slides produces the best quality of output - probably due to my lack of proper technique with negatives. Some of the new negative films were designed with scanning in mind and you may want to shoot a few rolls and see how things turn out. (If you can find the film any more).
Scanning Sofware
I used the bundled Polaroid software for a year before I upgrade to Silverfast - due yourself a favor and go buy a copy. It supports all the major scanners and it's feature set is outstanding.