Homebrew emulators VS VC games?

I use my HBC to play NES, SNES, Genesis, and Gameboy games, even ones available on the Virtual Console. Is there any benefit/downfall to playing emulators VS the Virtual Console? As far as I know, the VC games are just direct roms from the older iterations of the games (for example, in the NES Super Mario Bros, there's the Minus World glitch, which is still available in the VC version, but removed in the Gameboy Color and SNES versions).

AFAIK, there isn't really any gameplay difference.

The only difference is right now the VC N64 games are better than the emulated N64 games by Wii64. BUUUT Wii 64 is still a beta once it's no longer a beta or when the next beta comes out it may just meet the VC games.

Well, as for playability, I've noticed something odd in a few games:

Bionic Commando (NES): Freezes at a grey screen
Super Metroid (SNES): Loading the emulator menu randomly crashes after saving in-game
Mother 3 (GBA, translation patch) Audio skips from time to time. Only a hindrance in battle, as it needs rhythm in combat.
Alladin (SNES): Either I'm too good, or the game plays too fast.
Doom (SNES): REALLY bad framerate

1)Make sure you're using the latest versions of VBAX, FCEUGX, and SNES9XGX.

2)Note that VC cant do gba games or all but one of the games you listed

3)These issues sound unique to these games only. Post issues on their google code pages and Tantric will quickly resolve them I'm sure.

Also note, game-specific issues are typically present in the emulator itself, not just the port. So post them to the emulator team if the issue is present on the Windows version.