Specific Time Travel Games
There are several, and most are out of print. Pacesetter's Timemaster, BTRC's Timelords, FASA's Dr. Who, Cubicle 7's Dr. Who, Time and Temp.
I can't honestly recommend any of them, as I've only played Timemaster, and didn't much enjoy the game itself.
Cubicle 7's Dr Who is getting decent reviews, tho'.
And Time & Temp is still in print and PDF
Time Travel is mentioned as a key setting element in the Army of Darkness RPG, by Eden, and is a recurrent issue in the Red Dwarf setting, and so is mentioned in the Red Dwarf RPG. Both OOP, but still available in some channels.
Time Travel Supplements for Generic RPG's
BTRC's EABA has a conversion of Timelords to EABA. EABA's current settings are mostly fantasy and post-holocaust... or blends, and won't be too much help.
SJG's GURPS has a Time Travel, Infinite Worlds and Timeline worldbooks available. If you like GURPS, you have lots of worldbooks available to do the ends of the jump right...
My personal recommend is EABA, but in all fairness, I playtested EABA. If you need worldbooks to get the endpoint flavors right, do GURPS.
Other Generic Systems Notes
In general, if you have a favored generic engine, adapt your favorite paradigm to it, and go forth. You'll have more fun that way, I believe, because you'll not be fighting the engine... at least not too much. The important elements are that it have sufficiently good melee rules and language rules to account for the time travel issues, and robust enough character generation to enable you to generate target-time locals as well as prime-time-point characters. It really helps to have good vehicle rules if the 20th C or later are potential target times, and a good natural critters bestiary including riding beasts.
Hero System by Hero Games is quite capable of doing a time travel game right out of the core book. The Hero SYstem Bestiary is exquisite, and the core includes vehicles and common enough mounts; the medieval weapons are thin, but Fantasy Hero provides plenty, as does the Martial Arts book.
BTRC's CORPS and EABA are both capable of doing the time travel game right out of the core, as well. CORPS is PDF Only, and no longer actively supported. Both are short on worldbooks.
GURPS should work fairly well right out of the core books, too, but lacks vehicles in the core. Low Tech is also a great choice to have. The core has some riding beasts, and the Bestiary book many more. This is probably the best supported system.
Masterbook can do it, quite well, but lacks a vehicle design system. TORG setting books are fully compatible, providing a good source as well. (TORG is essentially Masterbook 0.5, and Shatterzone is Masterbook about 0.9, with the released Masterbook being 1.0...) TORG also works; TORG is a game of invading realities, and ranges from dinosaurs to space cruisers in one game...
FUDGE and FATE: I'm not aware of any specific timetravel versions of these engines, but neither takes much more work for time travel than any other multi-book system. Fantasy and Sci-Fi versions for both have seen print, and many variations of FUDGE are available online for free.
Cinematic Unisystem - BTVS, Angel, Ghosts of Avalon, Army of Darkness - enough medieval crunch factor in all these to do the primitive well. None of them does vehicles well... but all do combat really well, and have short enough skill lists that it's easy to generate characters for either end of a time jump.
Mongoose Traveller - MGT has a surprisingly decent medieval weapons list, and if one buys the 3rd party career books, plenty of low-tech careers. It's due to some setting artifacts (namely low tech worlds in a space opera setting, and use of blades to avoid damaging hull integrity), so the list is minimal but functional, and varied, including spears and halbeards...