This tip courtesy of Calligraphics.

I recently helped troubleshoot a large scene file to determine what was causing the excessive file size (130+ mb). It turned out that there were hundreds of orphaned or empty transform nodes. It seems that as you model you may be leaving behind a lot of no longer needed information. One of the things you should try doing is a scene optimization. This is accessed under the File menu. As the image below shows, there are several things that Maya can automatically try to fix for you. When run on that 130+ mb file I had it bought it down to just over 90 mb. So this is good place to start when you have those really heavy scene files. One note of caution though... optimize is not undoable (Maya will even warn of this before it optimizes).