I really can't pick one. There are many that I like, and several that I love equally.
One, as kari77 mentions, is Weapon, by Matthew Good. Episode 309. She mentioned the lyrics that stood out to her. For me, it's different ones, such as "Careful, be careful" and "This is where the world drops off." These say a lot about Brian and Justin's new/old relationship. Careful can mean a lot of things, such as tread carefully, don't make the same mistakes. "This is where the world drops off" is a metaphor for Brian and Justin's way of shutting out evereything around them. When they're alone, they almost exist in a bubble. There's no one but them.
Another song I love is "Break 4 Love", by Pet Shop Boys, used in 209, on of my favorite episodes. It's where we're treated to Justin's Snoopy Dance Of Love. It's fast, sexy and fun.
The thord one that comes to mind is Sola Sistim, by Underworld, used in the closing scenes of 306, when Justin's sitting at the bar in Woody's, after having seen Ethan leave with "the music student". It's slow, seductive, and rather melancholy. Two lines that jump out at me were "My devious nature, make it go away" and "Beautiful, broken, my crystal fingers". They describe perfectly both Ethan's betrayal and Justin's shattered illusions. Interestingly enough, both Ethan and Justin's art are made by their fingers; they each wear a promise ring on their ring fingers. Justin is seen playing with the ring, and Brian taps it to remind Justin of his broken symbol of true love.
Last, we have "Get Some Lovin" by Kristine W, from 310. I just love the energy of this song, the energy of Babylon, crammed to the rafters because of the crackdown of Liberty Ave by Stockwell. You can almost feel the heat, the thumpa-thumpa, smell the sweat. Dancers dressed as cops, dancers wearing handcuffs, and a good time was had by all.
All of these songs enhance the scenes for which they were used, and makes my viewing experience that much more pleasureable.