1. Awstats back in cPanel would be cool.
2. A nice feature for people that need many SQL databases might be to instead of limiting the databases, deduct the size of these databases from the user's disk space and the same for bandwidth (deduct amount of information read from database on each user connection). You could still limit the number of databases, but perhaps to a higher number like 10 or something, still preventing obscene amounts of databases being created.
3. An option for users to auto-include the appropriate ads at the top/bottom of each page by simply checking a box in a control panel. When a user is suspended for not having ads, perhaps an account manager can put them on "probation" by forcing this option to always be on.
4. Someone else mentioned this in another topic: Purchasing extra subdomains (or parked domains, or anything limited like that) via the shop. Might be a bit tricky and would likely require account manager to "manually" add such purchases to the user's account.
5. Monthly-mailed statistics, including bandwidth, space, SQL, etc. usage emailed right to the user's inbox via email when this option is enabled. However, this might be a bit taxing on the servers depending on how many people subscribe.
Just ideas, if I think of anything else I'll edit or post back.