The few games confirmed to be coming to the VC are Metroid Fusion, Yoshi's Island: Super Mario Bros. Advanced 3, and Mario & Luigi: Superstar Saga.
Considering that Yoshi's Island: Super Mario Bros. Advanced 3 is a remake of Yoshi's Island for the Super Nintendo, it is safe to assume that other GBA games that were just remakes may also be seen on the VC.
While many fans have asked for the Pokemon games to be brought to the VC, it is doubtful that they will be joining the group of games making their way to the VC. Though with the new Pokemon Bank application, it could be in the best interest of Nintendo and Game Freak to make the games available.
It is also possible that at some point these games make the transition to the 3DS, as many fans are hoping.
Personally I look most forward to revisiting the BeanBean Kingdom of Superstar Saga, which is not only one of the best Mario RPGs, but one of the best RPGs period. What old handheld games are you looking forward to playing?