Running the game in 60Hz is going to increase the framerate from 25 to 30 FPS (in other cases from 50 to 60 FPS) if I remember correctly.
Edit: I've played Starfox 64, Mario Kart 64 and Paper Mario on my Wii so far and I've never noticed any drops in performance. I'm quite sure Majora's Mask ran at a higher framerate than its prequel, though.
I remember reading that MM had a worse framerate than OoT, because Nintendo improved the textures / draw distance / area size / enemy count a lot, at the cost of a higher framerate. That's why I'm not sure if the VC version runs worse than the cartridge, cause MM was a low framerate game anyway, if I am correct.
The lag thing is a different issue though... I've noticed it with SMW and Zelda II, too, and on other TV's as well. It's really annoying, imo. I wonder why no one else ever complains about this.
Currently playing: NSMB (Wii)