I have no love at all for Shelter, and I actually went to see it at the theater when it first came out. I know I'm in the minority - it's been called the best gay movie ever made by more than one critic - but I find it to be completely vacuous and insipid, although very prettily filmed (not a surprise since writer/director Jonah Markowitz typically works as an art director on films). Sorry, but if I had no more problems to deal with than the kid in that movie, I'd have had a much, much cushier life - and I'm guessing most everyone here can say the same.
A film I like better, which came out one year earlier and had a suspiciously similar plot - kid from the wrong side of the tracks explores his sexuality while trying to get into art school - is Vacationland. It's not near as pretty a film in any sense of the word - much lower budget, more amateurishly filmed and acted, rougher in look and in plot. But it also plays much more true to life. And while the ending isn't storybook, I found it very satisfying.
A funny contrast - while Shelter chose a title that seems overly melodramatic considering the softball plot, Vacationland went for irony in the opposite direction.
As for a more mainstream gay movie, you can't do much better than The Broken Hearts Club. It's not exactly a romantic comedy and doesn't have exactly a happy ending, but it's one that'll leave you feeling good about being gay.