To batch process AI to EPS files, do the following (NOTE: I've got Illustrator 10 in front of me right now, so maybe some of these instructions might be slightly different in CS. I'll check later and confirm).
1: With no documents open, open the Actions palette (Window > Actions)
2: In the fly out menu on the Actions palette, choose New Action and give it a name (say, AI to EPS)
3: Click Record.
4: Open one of your AI files
5: File > Save As... and save it as an EPS file.
6: In the Actions palette menu, click "Stop Recording".
Now you've got an action that can be reused time and again. Put all your AI files into one folder, and create another folder where you want your EPS files to go. In the Actions palette menu, choose Batch...
In the dialog that appears, choose your action (AI to EPS) and make sure Source and Destination are set to Folder. In the Source section, press Choose... and pick your folder with AI files. Also check the "override Action "Open" Commands" check box. In the Destination section, check the "Override Action "Save" Commands" box.
Click Ok, and go make some coffee. I would suggest just putting a few files in the source folder first, just to make sure everything is ok. There's nothing worse that finding out after an hour that they've all been saved with the same file name....