What goes in the loop? What is played live? It depends on your situation. Do you want to make it "just like the album" or do you want to enhance the album cut, adding some creativity? Each might be a valid choice.
Here's a loop I made for Beautiful Jesus. The arrangement is just like the album, but I've added some favorite patches that give this the UCC "brand."
Also, here's the link to Matt's blog. He sparked my thinking on bwack's forum.
On another note, we did Salvation Is Here this weekend, and used igniter media's video. If you haven't checked them out, they've got some pretty cool stuff. Especially check out their video for Jesus Paid It All.