Good points, Enhas and Tyrannus:
RE: the Fry/Leela "Phil" thing - I'm trying to remember which fic that originated with, because once it started it really caught on like wildfire.
RE: Bart's future!job - I'm with Chris in that I like that version of Future!Bart's life the best, which is why I use it often. If the flash-forward in "Itchy and Scratchy: The Movie" counts for anything, Bart really will end up on the Supreme Court, and that's the closest we've come to proven!canon future for him. And, like Chris pointed out, anything's better than Bart To The Future!Bart (and on top of that Futuredrama!Bart also seems to key into Lisa's Wedding's version of his characterization).
I've always presumed Jessica's written as having green eyes because it taps into the femme fatale stereotype.
RE: Maggie as Bart+Lisa: That's become a common fannon thing over time, hasn't it? Can anyone remember its origins? The best thing about Maggie's characterization nowadays is that we can draw from recent canon (Simpsons Movie, for instance) and use it to sum up who she might be in the future with more authority. When I put together Future!Maggie for Wavingverse canon, for instance, I tried to model her life closely on Lisa's Wedding-canon Maggie (chattery, dirt-bike loving, "a bit of a hellion but she sings like an angel".)
Maggie being a Bart/Lisa mix isn't exactly out of character, just bland, especially since Maggie's character is so flexible. She could become so many different things, even a sociopathic assassin and it wouldn't be that odd, or at least to me.
...First person who writes a Simpsons/VB AU crossover where Mol has to pass the torch on to young Maggie gets a pony

And here's a bit of fanon I think I started: Fry calling Leela "Leel". I wrote that back in DS and it's since popped up in a few other folks' fics.