The letters from the first season had something to do with the Alias Online web game thing. (I can't remember the actual name.) I'm not sure about Season 2 or 3; there's definitely some signifance, I just don't know if it's a code that will have something do with the show itself, or another game or something.
By the way, most Alias sites refer to those letters as "push-throughs." There are quite a few places where you can view all of them so far.