If the file has DRM there is no way to convert files without, at least, violating the Terms of Service.
If the file has not got DRM, there are a number of solutions available.
You can just send it through Amazon using the kindles email address or, even easier, the Send to Kindle applet. Send to Kindle for PC is available to download at www.amazon.com/sendtokindle/pc and Send to Kindle for Mac is available for download at www.amazon.com/sendtokindle/mac.
If it's PDF, you have to send it via email and be sure to put the word "convert" as the subject.
You can also use web based apps -- do a search and you'll find plenty.
Many people here use Calibre for conversion as well as a database of their books.
MobiPocket Creator is also quite good, but I don't believe it's supported any longer: you can still find it, but there aren't going to be any improvements.
Note that converting from PDF is always going to be a bit problematic without putting a lot of work into it since the format is designed to be an 'end product' that looks just like this and not a re-flowable, adjustable format. If there's specialized formatting, charts, pictures, etc, the results are never better than adequate.