Time travel stories can be fun, but require a lot of planning by the GM. I've run one or two major stories so far, with more to come.
In the first time travel story, Time Master sends the villain Omega back to 1985 to recruit the heroes to stop the future Master Control, who is experimenting with time travel. Omega, a villain the heroes have never seen before, is successful in recruiting them, and takes them back to 1993 where they attack Master Control's secret base in the Colorado mountains. The heroes meet a team from this future era, who call themselves Steel Justice. Steel Justice was formed to honor the PC hero team when they were destroyed by the villain Omega in the early 1990s (a fact which Omega neglected to tell them when he recruited them). Omega seeks to stop Master Control as well as his past is somehow threatened by Master Control's time traveling into the past. The heroes and Omega manage to defeat Master Control and destroy his time machine in the end. During the course of the story, the heroes learn things about their futures to come (two are believed dead by 1993, one has a daughter with a villain(?!?), one is married, one has a terrible accident, and of course, the whole team is disbanded/defeated by Omega, etc). The heroes are returned safely to 1985, wondering if they can avoid their destined futures.
Since I ran that story, I've worked hard to work in each of the futures revealed for each of the heroes. So far, it's worked well. The heroes think they can alter their futures and avoid their destinies, but in the end, Fate always steps in and surprises them with their fortold future becoming a reality. The current time of the campaign is 1988, and thus far most of the heroes have had their fortold futures come true to some degree. Oh, and Omega has finally made his first appearance in the current continutity of the campaign by sending his emissaries to battle the heroes. Trust me, the heroes are worried that Omega really will be the end of them.
Another story involving time travel that I have run involved the daughter of one heroine and a villain (see above - her perdicted future came true!). The villain stole the child and used a time machine to return to the early 1960s. The heroes could not follow back in time, but decided to track down the present day version of this villain. Well, it turns out, he was killed when struck by a car in 1963. They investigated what happened to his daugther after he died, but could not find out who raised her since 1963. It's now 25 years later, and the daughter is a grown woman. The players don't know it yet, but the daughter is actually a woman villain they have fought several times during the course of the campaign; a villain who has done unspeakable things and they loathe her! Wait till they find out the missing daughter is actually one of their most hated foes! I'm so evil!
(Note: some of you may recognize part of this story as similar to a plot used during the 6th season of Xena. Well, let me tell you something, I came up with this story a whole year before the Xena writers did! Bastards stole my story! )