FrameMaker is one of the most successful programs around at being cross-platform, given all the work it has to do. But there are issues to be aware of and much you can do to make for a successful cross-platform experience.
For the purposes of this discussion, there are two kinds of fonts: fonts that do have the same name on both platforms, and those that don't have the same name. Fonts that do have the same name are a no-brainer, and will not cause a problem. This section, therefore, addresses fonts with different names.
Mac to Windows: A Mac file moved to Windows can be dealt with quite easily using Frame's ini file (called maker.ini in regular FrameMaker and fmsgml.ini in FrameMaker+SGML).
Windows to Mac: Sadly, when it comes to FrameMaker, fonts in Windows are easier to deal with than fonts on Macintosh. I said "sadly" because I do like the Mac -- a lot -- but the Mac versions, at least up to and including version 6, don't have that handy ini file that you can customize to provide a handy "if I don't have font X then use font Y" tool. You can, strictly speaking, use ResEdit to modify the code, but I'll not address that for now. (Actually, it's been years since I had to do it, and I'd need to freshen up a bit before I talked about it here.)
For information on using the ini file to rename fonts, see "Mass conversion of a font."
As long as you stick to common file formats like TIFF, EPS, GIF, and JPEG, you are okay. One to avoid at all costs is WMF and, although it's not quite as bad, EMF.
On the Mac side you may encounter the PICT format, which is a format used for both artwork and for the preview in some EPS files. You will need to work with your Windows counterpart to work out a resolution (who is going to fix things).
If you're using subdirectories for your graphics, they may or may not require relinking when moved to the other platform. In most cases, if any relinking is needed at all, you will only need to relink one file -- if the rest of your graphics are in the same directory, Frame will find them there and not bother you for the rest. On occasion I've seen files that actually had to be relinked by hand, but it's rare.
The Macintosh does not require file extensions. In the strictest sense Windows does not either, but for the most part we'll agree that it does. When files without extensions are moved from Mac to Windows and you want to rename the files, you should rename them within the book file, as Frame will automatically update necessary references except those within certain types of markers.