Most applications do no seem to clean up files placed on the SD card when they are uninstalled.

How can a developer provide users with an option to clean up the app-specific resources on the SD during the uninstall process?

This has been asked before (elsewhere). In other words, whether there's a system hook that allows the registration of a routine to perform app specific clean-up work at uninstall. No answers were found though, and I don't think such a hook or other means exist. If you know an app that positively removes files in /sdcard at uninstall, you may need to contact the dev directly.

Outside of that, /sdcard seems a bit of an unwanted child in the Android world. On the conceptual level, I consider it best to keep data server side, which scales well, but introduces a new dimension of effort. If the data doesn't amount to much, you can keep it on board in a sqlite database.