The title's pretty literal here: Boy Meets Boy is a book in which two boys meet. It's also a reference to a classic, well-worn plotline you'll see if you watch TV or movies for, like, a night: boy meets girl, boy loses girl, boy gets girl back. Think Ross and Rachel on Friends, Andie and Blane in Pretty in Pink, and a little ditty called Romeo and Juliet. In other words, you've seen this story so many times it probably makes your eyes glaze over by now (unless you're a sucker for romantic comedies, in which case bring it.)
Boy Meets Boy however, is a phrase that makes you stop and think for a second, kind of like a wedding card in a gift shop that says Mr. and Mr. might make you glance again. Just in case you weren't sure the title referred to a romantic relationship, it's spelled out in candy hearts on the cover, removing any doubt.
The use of a well-known romance cliché to normalize a gay relationship was actually pretty subversive back in 2003. The world was becoming more tolerant of LGBTQ relationships, but it was by no means the norm. Not only did David Levithan write some beautiful sentences, he gave LGBTQ teens a positive representations of themselves in YA lit, and in doing so he might have even saved a couple of lives (this book came out years before the It Gets Better Project began).