Not in any order:
The Outsider - A Perfect Circle
Imagine - John Lennon
Blackest Eyes - Porcupine Tree
Trains - Porcupine Tree
Anesthetize - Porcupine Tree
Jambi - Tool
Lateralus - Tool
Jesus Christ - Brand New
Kicking Your Crosses Down - Circa Survive
How I could Just Kill a Man - Rage Against The Machine (can't help feelin' like a gangsta sometimes

)
Edit thought of more*
Aenima - Tool
Swing Life Away - Rise Against
Second Life Syndrome - Riverside