If you have it set to auto frameskip, it looks really good most of the time. Sometimes you will be able to see the difference, especially if you are playing on a TV, but it isn't too bad at all. Take Final Fantasy for example, the rom of FF 1 and 2 together plays at 100%, but the roms of 4 and 6 (haven't tried 5 on GBA yet) play very well, but you can see the skip during battles and while on the airship. Once again, by no means very bad, but just a bit noticeable if you are super familiar with the games.
Still most games look and play great. You'll probably want to stay away from the 3d heavy titles like doom or some of the racing games, although Mario Cart plays perfectly.
As for the ones you mentioned, Megaman Battle Network plays just fine. Golden Sun 1 and 2, on the other hand, run very slowly. Tales of Phantasia, on the the other hand, a game this is sort of similar, plays just fine.
Most of what you will try with GBA will be fine, but there are a few roms that won't work or run slow. Still a pretty good emu though.