Oh, in the dim and distant I ran a lot not in the OTU. The only thing that was coherent enough to describe as a setting was a version of Blake's 7 but alas, I can remmeber very little and the notes went west over a decade ago.
I have the beginnings of an adaptation of B5 to my CT/MT/T4 hybrid, and the later incarantaion of "the Nearer Stars" (my homegrown 2300/CoC game) used a stripped down version of CT/DGP.
Moving away from the OTU is easiest with FF&S: it explicitly deals with variant technologies, but since I loathe the GDW house system (and never got a copy of the T4 version) I have never used it in anger. Variant FTL drives are probably the most obvious difference between settings, but given the core simplicity of CT/MT/T4 with thought it can be adapted to a very wide range of settings successfully. Certainly "San Jacinto" (the last game in my "the Nearer Stars" setting) worked very well.
Personally, I'd love to see a coherent write up of C J Cherryh's Alliance - Union - Compact books as a Traveller setting: the tech level is _ideal_ for Traveller, the culture (communications at the speed of ships) is very Traveller and teh gritty feel an excellent fit IMO...