I second the suggestion to make a run of Jurassic Park.
I'm surprised that nobody mentioned Battletoads & Double Dragon -- that would be a sight to watch. Seeing a run of Batman Returns would also be great. And Contra Force? Man, that was a great game! Not sure about how speedrunnable is New Ghostbusters 2, but it was a very fun game and I'd love to see a speedrun of it. Monster In My Pocket is definitely a game that should have its own run. A run of Gekitotsu Yonku Battle would be a blast to watch.
Also, what about the classics -- Battle City, Adventures Of Lolo, Karateka, Yie Ar Kung-Fu, Balloon Fight, Nuts & Milk, Bomberman 2, Lode Runner, Gun Smoke, Mappy, Wrecking Crew?
I'd also love to see runs of POW - Prisoners of War, Mighty Final Fight (2 players), Double Dragon 3 (2 players), Super Jetman, Robocop (including second and third Robocop games), Captain Planet and The Planeteers, Donald Land, Mitsume ga Tooru, Saint Seiya - Ougon Densetsu Kanketsu Hen and Terminator 2 - Judgment Day
All these games are very fun to play and watch (at least for those who played them...), so, as you can see, there still is a lot of NES games to speedrun. After all, it's not only about speed, it's also about entertainment, right?