RPGmaker transitions are pretty much limited as to "tell" a story by themselves. Of course, there are some classical transitions, such as "teleport -> fade out & in" or "Dream/faint -> pixelated" and such, but, as far as you get the map changed, that is the point of the transition. Of course you could try making something with that, but the player hardly would notice, and, in case he does, it wouldn't matter too much.
As for what takes you to the other world (a.k.a. teleport objects/tiles), yes, you can try that. In fact, it would be nice to see some kind of game made that way. I just though about Alice in Wonderland; you know, you go for the rabbithole and that; how the world transitions happens in that book is a good example that could easily be applied to these games. However, it wouldn't be the main point, and, in my opinion, they would not "tell a story". 'Twould be nice nonetheless, but they aren't the central point because the player's set of mind would be focusing in something else rather than the teleport, like "Right, I got to this bloody place through a corpse, but what about it?".
I think the best example of transitions you're looking for, that give you a sense of what the location you're visiting is, is OFF's transitions between zones perhaps. Each transition gives you a sort of overhead view of the zone and its music giving you a sense of what the location is like.
I haven't played any fangames in quite some time but I do know it's actually quite common for there to at least be one transition per game that has an object of significance, when you look at it you know for a fact you're going to a certain area. .flow's apartment buildings via the tiny concrete box is the only one I can think of at the moment.
I'm with above though, players might not get meaning from it other than it being a pleasant detail.