Amazon has a conversion service via e-mail, see
Sending Personal Documents to Kindle. Since the Kindle 2 now supports native PDFs, you must type "Convert" in the subject of the e-mail when you submit your personal document to your @kindle.com (or @free.kindle.com) address. It will then be converted to AZW (MOBI) format.
Windows MobiPocket Reader will do a similar conversion on your PC (import PDF, export MOBI). Calibre can also convert PDF to MOBI for the Kindle.