Knowledge Ecology Online has an interesting and up to date survey paper Selected Innovation Prizes and Reward Programs. In spite of the word "selected", it's pretty comprehensive if you're just looking for the most prominent innovation prizes. It covers prizes, organized into categories like "Aviation and Outer Space" in the TOC and by date in the main matter, from hundreds of years ago up through today - or close enough. Here's their announcement of the paper.
To show how active they've been, especially in the area of medical prizes and patent debates, here are some other updates:
Feb 8 GWU & KEI Workshop on Medical Innovation Prize Fund
Jan 28/9 KEI & UNU-MERIT Medical Prize Fund Workshop
They also have some new papers and links to prize proposals, but I'll refrain from mentioning them individually until/unless I get a chance to read them. Check the site or their page Prizes to stimulate innovation if you're interested.