Some of these are alternate traveller universes (Twilight Sector is one example), but some are part of the OTU albeit in a different time period. Good point, though.

There's mention of some fan-authored settings here: http://forums.sjgames.com/showthread.php?t=111482, though I don't recall seeing any such settings posted online. If you know of any, please let me know where to find them. As far as sorting such settings out, I'd suggest you first classify them into one of three categories:

Conforming: A setting that does not contradict the OTU, although it may be set in a time or place somewhat removed from the OTU. TNE would be an example, even though that timeline was subsequently contradicted by GURPS:Traveller.

Variant: A setting that mostly matches the OTU, particularly in spirit, but which deviates in some important ways, such as the Constitutional Imperium that Richard has proposed.

Alternate: A setting that is wholly incompatible with the OTU, such as the Twilight Sector.