The author of Rapture Ready has posted a playlist of his "10 great Christian rock songs. Really." I agree with some of his selections, although many are after my time in the scene. (I used to be a regular contributor to rec.music.christian, which is where I met some of the people who are still on my friends list.)

I would substitute or include.

1. Chagall Guevara - Not the Christian version of Marilyn Manson, as you might expect. (Although Marilyn was raised Pentacostal. As was Frank Black of the Pixies, in whose honor I am taking the day off.) It's a Steve Taylor project. Steve was a new wave Christian rocker back in the day, and is now a Christian producer. (Including for Sixpence None The Richer, a band on Daniel Radosh's list.) Late '80s alternative, with a song showing up on the Pump Up The Volume soundtrack alongside the Pixies' "Wave of Mutilation".
2. Tonio K. - Amazing songwriter from way back. Co-wrote "Love Is" for Vanessa Williams, but don't judge him by that. (He claims it was for Tom Waits, and even if it's not true, just imagining it is six tons of awesome.) His songs have shown up on some of my favorite movies, from Real Genius to True Romance. His own albums are great, bouncing back and forth between sardonic and downright sappy.
3. Victoria Williams - Another amazing songwriter. If you can't stand her freaky little girl voice, check out the tribute album that her friends in the music industry put together after she was diagnosed with MS. You've probably heard Pearl Jam's cover of "Crazy Mary", but for my money Evan Dando's version of "Frying Pan" is the best.
4. The Choir - They've slid into producing and boring "praise & worship" shit in the last decade, but in the beginning they were one of the most introspective and interesting Christian bands out there. They still work with nearly everybody doing anything interesting in the Christian music world. And check out those gas prices!
5. Sam Phillips - Went the other direction. Started out as a manufactured Christian pop singer and ended up breaking out. Started getting really good with '87s The Turning. I've been listening to her ever since. I just bought her new album.
6. Daniel Amos - Been around since the '70s, started as a country/rock band and ended up doing just about every kind of music there is. No, really. Currently in the alt.country arena. My favorite is 1986's blippy Fearful Symmetry. Jonathan Coulton is actually a fan of Terry Scott Taylor too.