Not a long one, but DOOM QUEST has always been a favorite of mine. So has that AVENGERS : FOREVER that I know you have, but that is anything but short. Basically any AVENGERS story with KANG and any FF story with RAMA TUT (EDIT - Or Immortus ... ya know, same guy)
Right before I came back to comics, or right when, I forget ... ahem, anyway, there was that DC ONE MILLLION thing happening that I think was a time travel story, though I never read any of it.
Of course, a lot of DC ELSEWORLDS also have the time travel feel to them, though not really "traveling" anywhere.
And also not really what you're looking for, but Byrne's GENERATIONS had to do with Bat and Supes actually ageing and seeing them through the genreations. That was kinda good.