Off the top of my head I think you mean "War Without End", B5 intercepts a transmission coming through the time rift in Sector 14, from a B5 station of an alternate future which is being destroyed in a week, unless our heroes do what it is they must in that episode (Plot removed to prevent spoilers)
No there wasn´t any alternate-universe or time travel episodes in the series other that WWE , this is , after all , Babylon 5 not Star Trek .
However , if you like to read fanfiction , you can find a certain number of alternate babylon 5 stories through the net , from the Dark mirror unverse from Gareth Williams to several others .
I think you must be remembering some Fan Fiction Golem, appart from WWE, and the various jumps around the timeline, I can't think of anything like that in B5. It does sound a lot like the original Mirror Univers episode of Star Trek : TOS though.
You're not thinking of "The Deconstruction of Falling Stars", are you? Last episode of Season 4, it shows four different glimpses of the future of the B5 universe (100 years on, 200 years on, 500 years on and a million years on, IIRC).