The song in the very opening scene with the first victim on the roof is:
"Sea Lion" by Sage Francis


The song in the scene when Dr. Brennan's Dad burns Deputy Director Kirby, in the same way as the beginning, and then Booth finds him is:
"Running Up That Hill" by Placebo

http://www.tv.com/bones/judas-on-a-pole/episode/896334/summary.html?tag=ep_list; title;10
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