Probably your questions are better answered in an Illustrator forum rather than here in a Mac/Windows forum. Adobe's website would be an excellent place to continue your research.
I can say with a reasonable amount of confidence that fonts will probably be your biggest issue. While you may have "Arial" on both your Mac and Windows systems, they may not be identical versions; the metrics for each version may be different because they're from different foundaries or they were produced at different times. This may produce different kerning and lines of text may wrap differently. (While I don't have any experience with OpenType, you should look at this as an option. The same OT font files can be used on both Macs and Windows.)
As far as the files themselves are concerned, you'll find that a "CS" file on Mac is almost (if not exactly) the same as a "CS" file on Windows. You may run into some issues if your versions of Illustrator vary (say from CS on Mac to CS2 on Windows).
Hope this helps! bill
1 GHz Powerbook G4 Mac OS X (10.4.4)