Toward the end of the game at least, the functional fuel depots seem to mostly be concentrated in the lower left-hand corner of the Galaxy Map. In the following image, systems with fuel depots accessible directly from Mass Relays are circled in green (six total):
As you may already know, most systems will also contain fuel depot wreckage sites that you can scan for, for a one-time fuel bonus. However, if you're just looking to quickly top off your tank, visiting one of the above-circled systems is the way to go.
In particular, I believe Annos Basin (to the left of the selection cursor on the map) is available to the player for most of the game, and is never marked as being Reaper controlled.