after recently recompleting the thieves guild (oblivion), i wondered, are/were the guilds in Morrowind and Cyrodiil different branches or completely seperate from another?

To my knowledge, they are separate. They were founded by different people, so I doubt they're affiliated with each other in any way.

the fighters and mages guilds are the same, thieves different.

Dark Brotherhood is the same organization as seen in DF, MW, and OB.

I'm fairly certain that the Fighters and Mages Guild as well as the Dark Brotherhood seen throughout all games are supposed to be the same organization (The Dark Brotherhood in particular isn't really a generic enough name to have multiple factions with the same name in the same world, it would, on the other hand, be more plausible for there to be more than one Mages Guild or Fighters Guild.) any differences in how these guilds operate is likely either due to different management in different times and provinces, or inconsistencies between games (It certainly wouldn't be the only way where the games haven't been consistent.) now the Thieves Guild on the other hand I am not so sure of, everything I've heard certainly gives the impression that the Thieves Guild in Cyrodiil is different from the organization seen in Morrowind and Daggerfall, and I don't see any way to reconcile the aspect of the Guild being assumed to be a myth by many with how it was portrayed in Morrowind, where the existence of the Guild, as well as the fact that it was at war with the Commona Tong, was widely known and the Guild would openly do things in local taverns instead of having secret meetings after midnight in a lonely corner of the waterfront, aside from assuming that they're completely different organizations.

Hmmm, the Morag Tong would be pretty much restricted to Morrowind, right? It'd be illegal for them to kill outside the province?

The Morag Tong is indeed outlawed and hated outside Morrowind. Within Morrowind, I think the Empire looks the other way, as the lesser of two evils (the greater evil being continual House wars). The assassination of Reman III pretty much ended any kind of toleration the Empire might extend to them outside their home province.

They are all the same, but regional guilds have different degrees of independence from the centre.

Morag Thong, apparently, was protected by Armistice, but only in Morrowind and only for dunmeri:
"...of course non-Dunmer are forbidden to hire or to be marked; some say that Tiber Septim himself negotiated this arrangement with the Morag Tong at the time of the Armistice" - "Skeleton Man's interview".

arch mage traven said the mages guild was originally based in the summerset isles

Galron was originally a pijjic, but hated how elitist they were, so he left on good terms and began the Mages Guild, which eventually expanded to Cyrodiil, and became an imperial sanctioned guild.

what makes you think that the Theives Guild is different from the one in Morrowind, which is different from the one in Dagerfall? Some ranks are even named the same; and I assume that Master Theif is like "regional manager" where as the Gray fox is like "Chairman of the Board of Trustees"

Thanks alot for all the replies.