Yarin, it at least partially depends on why the PDFs don't work in the first place. If you can use them after re-saving with Apple's (quite bad) preview PDF code, you should be able to get the same result using a number of different tactics:
-) Use an actual PDF library to open and save the PDF files (libraries from Adobe and Global Graphics come to mind). These are typically commercial products but (I know the Adobe library the best) they do allow you to open a file and save it, performing a number of optimisations in the process. The Adobe libraries are currently licensed through a company called DataLogics (http://www.datalogics.com)
-) Use a commercial product that embeds these libraries. callas pdfToolbox comes to mind (warning, I'm affiliated with this product). This basically gives you the same possibilities as the previous point, but in a somewhat easier to use package (command-line use for example).
-) Use an open source product. I'm not very well positioned to provide useful links for that.
There is another approach that may work depending on your workflow and files. In graphic arts bad files are sometimes "made better" by a process called re-distilling; you basically convert the PDF file to PostScript and re-distill the postscript into PDF again. Because this rewrites the whole file structure, it often fixes fundamental problems. However, it also comes with risks as you're going through a different file format. Libraries such as GhostScript (watch the licensing conditions) may allow you to do this.
Given that your files seem to be fixed simply by using preview, I would think a redistilling approach would be overly dangerous and overkill. I would look into finding a good PDF library that can automatically open and save your files.