Hi Nick,
Most of the time I use Canon Digital Photo Professional. This works well for me as it has white balance, cropping, sharpening, levels and noise reduction all readily at hand. It will also print directly from the RAW file and save changes to one image as a "recipe" which can be copied onto a batch of images to make multiple changes.
I recently acquired a copy of Phase One's Capture One LE - Apparently it is £99 to buy but I got a free licence with a Sandisc Extreme III CF. This looks very good, and probably better than Digital Photo Professional, but I haven't used it in anger yet - sticking with what you are used to is easier. It has had very good reviews in the photography mags and I would give it some serious consideration - particularly if you can get it for free.
If I want to get more involved I now use Adobe Elements 5.0. This gives multiple layers for adjustment, cloning, and infinite subtlety in rotation control. Adobe starts with the RAW file but seems to convert this to an intermediate Photoshop file fairly early on for subsequent manipulation. I don't believe this is detrimental to the image, as it doesn't compress in the same way as a JPEG, but I prefer to stick with the base file if I can.
JPEG is fine for snap shots but, it is a compressed file and any subsequent manipulation will cause further compression and ultimate image degradation. RAW works with the unaltered data from the camera but generally needs some post processing before it is ready to show or print.
Sorry guys for going off thread. I guess we should have started another post.