How to check which enabled modules are really used?
It sounds as if you're installing modules on a production site willy-nilly, just to try them out.  I suggest you stop doing this.  While people like me earn some of our living from helping the owners of such garbage piles sort through their wreckage, I'd rather get paid for building stuff than for cleaning up.

Instead:


Set up a staging site for testing stuff. Only deploy on the production site if it is proven useful.
Keep a log of everything you deploy on the production site, with details about when and why. Log also when you disable and uninstall, so you don't forget and make the same mistake twice.


The above is absolutely essential if more than one person runs the web site - but I've found it helpful even if there is only a single webmaster that does it all.

There is really no way of keeping tabs on "what you really use" automatically or semi-automatically. Configuration management is just one of the tasks a webmaster is supposed to do as part of a honest day's work.