I have written an app in VB (actually, VBA inside Access) that automatically moves files between the regular folder and an alternate folder based on checkboxes. Unlike iTunes, you can see a lot of info about each app, including its revision, its filename, its size, and its date. You can also sort by any of these. After you use my app to decide which apps will/will not sync, then you run iTunes and the ones you unchecked in my app will have disappeared from iTunes's list altogether (but they'll come back if you re-run my app and re-check them).
Is anybody interested in such an app? It's currently not polished for widespread distribution — but it could be.