Genkirindan - A vertical shooter from Taito. That has you flying through the past, present and future chasing the time traveling boss guy. What's cool about that game is that each stage uses the same music but altered for each time frame.
Final Fantasy Legends III (SaGa 3 in Japan) for Game Boy features a flying stealth-bomber looking time machine. Mega Man II on Game Boy had something to do with time travel plotwise, but I don't think it ever played a big role. Secret of Everquest involved time travel. Illusion of Gaia had some time travel elements IIRC. It's been a minute on that one though, so I'm not entirely sure if I'm remembering things right. Shinobi on 3DS involves time travel. Radiant Silvergun involves time travel. Final Fantasy features time travel. Final Fantasy XIII-2 has A LOT to do with time travel. The original Shining Force has some time travel (Max and Kane are from the future I think). Speaking of which, Fire Emblem: Awakening has has some time travel elements (and is still my favorite game to come out this year). 'Sall I can think of right now.
Terranigma on the snes had the whole create and make the world and towns prosper element. Going through the different time periods was pretty awesome couldnt go back in time I don't think in that one though.
