Beetle Adventure Racing needs a sequel. It's one of my favorite racing games, and I just loved the great course designs. I hope BAR shows up on the Virtual Console soon.
I want a real sequel to Chrono Trigger. I wasn't happy with Chrono Cross, besides the amazing music.
I don't necessarily want a sequel to Hotel Dusk since the game pretty much wrapped up the story, but I want the developer to make more adventure games similar to Hotel Dusk, maybe even set in the same world with different character (along with one or two returning characters just to make the fans happy).
We need Capcom to make a Resident Evil spin off series based on the Resident Evil 4 engine for the Wii, while continuing the main series on the 360 and PS3.
Star Trek Legacy was a decent game that needs a sequel if the developers can fix the issues the first game had. While the sequel could continue having all Trek eras, they should really focus on the Dominion Wars and have most of the missions based on DS9.
Skies of Arcadia is begging for a sequel, even if it's a Final Fantasy style sequel with a new world a characters. However, I don't want to see the current Sega develop a new SoA because they would most likely screw it up.
I love the Vigilante 8 series on the N64, and I can't wait for the XBLA version to show up. The developer needs to stop making the stupid True Crime games and make Vigilante 8 3.
Sony needs to make another War of the Monsters game. The first one was amazing, I would imagine that a sequel on the PS3 would be even better.