Idea #2645 postulates IMHO very needed tool for keeping your homedir tidy. I'd like to propose something similar in application but different in the way of operation.
Namely, we need the app - which should be a standard part of GNOME, installed and exposed to user by default - that would flush configured directories off defined classes of files.
The app would have initially only basic integration with system and GNOME environment - Trash, Nautilus thumbnails and the like. For other things mentioned in #2645 the programs producing those garbage should be able to register it with cleaner app. In case of non-GNOME programs this registration could be done with *-gnome-support (like firefox-gnome-support) packages.
The app's GUI should enable the user to check/uncheck the items s/he wants to purge.
Rationale: as is evident from comments to #2645 there will never be the one definitive list of garbage sources. Plugins would work of course but they require that user actually installs them, one by one as in Firefox case. Also, user must know about plugins so either we invest in making the GUI for searching and browsing plugins and in some entity that accepts and checks them or we just require the garbage producers to be well-behaved and specify what, where and how often needs to be cleaned.
While it would be silly to expect that every application maker for Linux follows this, we can expect GNOME to require that it's own apps will follow the suit. That would be enough (for a time ;) )