I know this may sound silly, but for anyone who's beat their heads against their keyboard because they can't save anything in Illustrator CS4 (especially older files that you've modified), I have discovered a simple solution that worked for me.
Open Illustrator CS4 and then open one of your older Illustrotor files. Then go to "File" and go down to "Save a Copy..." and save the file with the added "CS4" to the file name. Once you do that, the problem of not being able to open, change and save older (and even new) files seams to go away.
Don't ask me why it works, but it does. At least it worked for myself in Windows Vista 64.
Now I just need to solve the TTF's not showing up in all the Character menues, and I'll be stress free with CS4!!!
Good Luck! I hope it works for you too.
AKA - The Image Wizard