Applications in vs. applications to

When "to" is used, that makes "interactive media" the direct object: something/someone external applies eye tracking to interactive media.

When you use "in", that means "interactive media" is an adverbial: You apply eye tracking. Where? in interactive media, where interactive media is a collectivum for a lot of things, whereas in the other sentence it is a defined "object".

I would use in:

I’m one semester away from completing my master’s studies of the applications of eye tracking in interactive media.

As for my reason? It just sounds better. Applications to media doesn't make sense to me; applications in media does.

You have a string of prepositional phrases in this one sentence. You might consider rewording it slightly, to something like:

I’m one semester away from completing my master’s studies on the way eye tracking can be applied in interactive media.