Some differences between gnats and fruit flies:

Gnats are smaller, darker, and have longer legs and antennae than fruit flies.
Gnats tend to fly in swarms, while fruit flies fly alone or in pairs.
Gnats have small eyes that are hard to see, while fruit flies have big, red eyes.
Gnats belong to the family Mycetophilidae, while fruit flies belong to the family Drosophilidae.
Gnats are found around moist soil or potted plants, while fruit flies are brought in on healthy fruit.

And, from personal experience: gnats bite and fruit flies are simply a nuisance.