And I'll second Joe's high praise of Noteworthy Composer. It's cheap ($40 registration fee shareware), it's compact (< 800k install file), and has more features than a program its size and price has any right to. It doesn't have the fancy Serious Composer of Complex Orchestral Scores features of Cakewalk or Finale, but it's done just about everything I have wanted it to. Maybe the first version I downloaded didn't, but the current 1.70 beta has added staff layering, which makes it much more versatile.

So even if you use one of the scan-to-MIDI programs mentioned, you could do far worse than pulling the MIDI into Noteworthy to clean it up. It's a nifty music editor that will both open and save MIDIs, and take direct MIDI device input.

Shad