Differences vary from game to game.
Some PAL games are adjusted for the lower frame rate. For example, PAL Super Metroid plays at the same speed on a PAL SNES as NTSC Super Metroid does on a US SNES. (So apart from the protection, PAL Super Metroid plays 20% faster than normal on a US console.)
Some other games which are speed-adjusted are Mario All-Stars and Super Mario World. Neither of those PAL carts work properly on a 60Hz console; there is graphical corruption.
Another example is PAL Starwing (= Starfox). That only works properly in 50Hz mode.
One strange example is PAL Pilotwings. That will not work on a US console, even if the console is in 50Hz mode. But US Pilotwings works fine on PAL consoles. I'm not sure why that is.
For Terranigma specifically, I think it is adjusted in some ways for 50Hz operation. I have not played the Japanese version yet, so cannot say for sure, but... you tap the controller twice in the same direction to run. This is easier to do correctly in 50Hz mode. There is a little sub-game which involves tapping buttons very fast. This is probably only do-able in 50Hz mode. (Or maybe I'm just lame.) The timing of the intro sequence might have been adjusted to keep in sync with the music.
> Let's take Zelda III for example.
> What's the difference between the american NTSC and the european PAL version? If the PAL Terranigma cart ran in 60 Hz, then the PAL Zelda ROM should be able to run in 60 Hz with no problems... So what's the difference then between the PAL Zelda and NTSC Zelda, except for the protection code, or any other PAL/NTSC game?
I think US Zelda III does run fine in 50Hz mode. As one of the earliest games, there is no protection check.
-- Mark