The Debug Log Filters are defined in the Metadata API, but only for use when executing code or running tests, they sadly are not present as a deployable aspect. In terms of what your wanting to do, with a large number of classes. I wanted to do something recently to focus Debug Filter settings on a handeful of classes from a large set.
Basically I disabled at the top level all filtering and enabled for each class what I wanted, this seemed to work quite well for what I wanted. Here is what I did.
- Go to Monitoring > Debug Logs
- Click New and provide your User
- Next to the entry created for your user click Filters
- Switch everything to NONE and click Save
Then on the few classes that you do want logging for
- Go to Develop > Classes
- Click on the class
- On the Log Filters tab, click the Override checkbox
- Set the settings to what you want.
NOTE: I found the UI's for both the above steps to be a little flakey, so go back in each case and double check your settings have taken.
Hope this helps!