I believe that the two versions you mention are quite similar. There are some differences, but the core mechanics and game design are still basically the same.

Some of the differences I am aware of:
* The PC version lacks the music found in the NES version. Also, there are obvious graphical and control differences.
* The NES version (to my understanding) requires that you reach level 3 before leaving Scorpigal; the PC version has no such requirement.
* Locust Plague: In the NES version, encounters with this particular enemy are unfair; if allowed to act even once, it will likely wipe out your entire party (I believe this is due to the interaction of two programming bugs; one makes them deal 255 damage, and the other resets the round when one of your characters falls). In the PC version, Locust Plagues are more reasonable; if one attacks, you can expect the targeted character to take 9 or 10 points of damage.(or less if you have good AC), making encounters with them at least fair. (Note that they are still likely to act before you, however.)

Also, note that bugs and glitches that are found in one version are likely to not be present in the other.

(Also, the GOG version comes with some of the other games in the series, so I would say it's worth it.)