Question: After some unsuccessful uploads I ended up with a lot of loose files in craft/storage/runtime/assets/tempuploads

They show up in the asset list when selecting assets for new entry. How do I remove them completely from the record?

Tried manually deleting them via FTP and running "Update Asset Indexes" but that didn't work. Also tried "Clear Caches" options.

Answer: 
In Craft 2 the only real solution is to delete all the entries from craft\_assetfiles where the sourceId is set to `null`. 

The reason why there's no clear cache tool for these is because that might allow for deletion of Assets that were just uploaded by someone else who might be about to use them.

This is really far from a practical solution and we know that, but it's not easily improved in Craft 2.

Craft 3 will slightly improve things by adding a "Temporary uploads" Asset volume which will hold all of the current user's *leftover* Assets, allowing you to deal with them as you would with regular Assets.
If you've already deleted the actual files, you can try rebuilding the Asset Index (via Settings -> Update Asset Indexes