Umm... I was asked how I do my clean up in Photoshop.
It's fairly simple really and has more to do with your own skill and patience with a stylus than with any sort of program or technique.
I start out AT LEAST 300dpi. I throw a layer of white underneath whatever layer has the rough drawing on it. Then I lower the opacity on the rough layer.
I tend to choose light grey or blue for the rough drawing and deep red for the final line just so it shows up nice an bright on the screen. It's not as easy to judge line quality with black and white.
Ok, here's the secret...well, not really. Zoom in fairly close, make sure shape dynamics are on so I can utilize thick/thin lines and basically hold my breath and cntrl-Z until I get a line I like. Yep, that's it. I also kinda "sculpt" the line with the eraser tool to further tune it. Also, zoom out often to check on how the line looks as you draw.
BTW- see those squiggly parts in the line? They pretty much don't make much of an impact if you're working at such a high resolution. When you res it down for the web (72dpi) it's pretty much non-existent. You can work at 600dpi and res down to 300dpi for print to do the same thing but still maintain decent resolution. However, if you're looking to make movie sized posters or anything, just use illustrator, Flash or ink by hand.
Draw straight through the shape and erase accordingly. You lines will be smoother and more consistent.
That's pretty much it. No Jimmie Hoffa secrets here but I hope that helps.