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Well, I've gotten surprisingly decent results using Amazon's @free.kindle.com conversion service. But they only let you use it if you've got an actual Kindle and not just one of the apps.
You can also try tweaking some of the Structure Detection and PDF input settings in Calibre, though I've heard that of the freely available apps, Mobipocket Creator does the best job (I wouldn't know; it doesn't work on the Mac).
Or find a regular PDF to text/html converter which does a good job and convert to Mobi from *that* conversion. I think Project Gutenberg's Distributed Proofreaders have a macro up on their wiki that will auto-clean extra linebreaks and such from text and html files. Or maybe we have one here at the MR wiki; I forget which.
Also, you could probably automate the process for your already-converted books using a couple of command line scripts so all you'd have to do is point them at a containing folder and walk away for a snack. But that may require a greater level of computer fiddling than you may be comfortable with.
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