Gargoyle's Quest
Technically part of the Ghosts 'n Goblins franchise, there have been three games (four if you count the GB port of Gargoyle's Quest II) in the spinoff series. The series offered some pretty challenging and cool side-scrolling gameplay mixed in with RPG elements; back before RPG elements were all the rage. This series seems ripe for revival either as a Wii Ware/PSN/XBLA game, an iOS/Android release, or for the 3DS or PSP. I would like to see the basic gameplay kept intact (2D sidescroller with RPG elements), but bringing modern gameplay designs to the mix could make this a great series to see alive once more.
ActRaiser
The first ActRaiser was easily one of my top 10 16-bit era games. While ActRaiser 2 was a bit of a misstep, it didn't tarnish the name enough in my mind to make me think that the series should have been left for dead. With a bit more depth to the world building and some tighter controls on the action sequences, this game could be a massive hit on handhelds and mobile platforms.
Star Control
Whenever anybody asks me what franchise is most deserving of a revival, I will ALWAYS say that it's Star Control. Star Control II was a game way, way ahead of its time and is still a game I reference often when I talk about how to properly handle open world gameplay. Star Control III was not so great, but I think if you got the Toys for Bob team together again for a 4th game that they'd probably be able to recapture the magic. For those that haven't experienced the splendor of Star Control II, it's now free to download thanks to The Ur-Quan Masters project. Search online for it and get to enjoying this masterpiece.
E.V.O.: Search for Eden
It's basically a 16-bit Spore, and it was a lot of fun to play through multiple times. Combat wasn't always the game's strong point, but the evolution system was great fun to play around with on your quest to become a human and to enter Eden. If the series could be revived properly, it might be able to give us what Spore made us believe we were going to receive.
Strider
Somehow Strider got left behind after Strider 2 (even if the old time EGM staff felt it was a bit too easy), despite it being a fairly solid and enjoyable action game. The Strider Hiryu character is still well known thanks to his cameos. Maybe it's time to give ol' Strider another starring role.
Blast Corps
It's hard to have a discussion about Nintendo 64 games without Blast Corps being brought up at some point. The game was a joy to play, even if the controls often fought against you. The game would probably work really well in a simple mobile/handheld form or in a crazy effects-driven experience on consoles.
Jet Set Radio
We did get Jet Set Radio Future on the Xbox, so it has been too long, but with motion controls being all the rage, I think it's definitely time to see Sega put another one of these titles out. Give it to us, Sega and let Sonic rest for a short season.
Rygar
Rygar actually made a little comeback on the PS2 (which got ported to the Wii), but it was criminally overlooked. The game was really well done, but there was little to no marketing push behind it. Maybe God Of War's shadow was a bit too big for Rygar to crawl out of in the last generation, or maybe Rygar just came out a bit too early before the action game revival, but I hope we haven't seen the last of Rygar.
P.N.03
P.N.03 was cool, stylish, and actually a lot better than it was made out to be. The game had some glaring faults to it, but it was quite unique and I think pretty much everybody thought Vanessa Z. Schneider was a good character. The suit system was interesting and it fostered replayability. I have to think that someone like Platinum Games would know how to rock this game out right.