2000 – Mer De Noms

1."The Hollow" – 2:58
2."Magdalena" – 4:06
3."Rose" – 3:26
4."Judith" – 4:07

5."Orestes" – 4:48
6."3 Libras" – 3:39
7."Sleeping Beauty"(Extended Intro 5:02 LP) – 4:10
8."Thomas" – 3:29
9."Renholder" – 2:24
10."Thinking of You" – 4:34
11."Brena" – 4:24
12."Over" – 2:21
13."Orestes" (Demo) (Japanese Import Bonus Track) - 3:24

2003 – Thirteenth Step

1."The Package" – 7:40
2."Weak and Powerless" – 3:15
3."The Noose" – 4:53
4."Blue" – 4:13
5."Vanishing" – 4:51
6."A Stranger" – 3:12
7."The Outsider" – 4:06
8."Crimes" (Howerdel/Keenan/Freese/White) – 2:34
9."The Nurse Who Loved Me" (Edwards/Andrews) – 4:04
10."Pet" – 4:34
11."Lullaby" – 2:01
12."Gravity" (Howerdel/Keenan/Freese/Van Leeuwen/Lenchantin) – 5:08

2004 – Emotive

1."Annihilation" (Crucifix) – 2:13
2."Imagine" (John Lennon) – 4:48
3."Peace, Love, and Understanding" (Nick Lowe; Elvis Costello) – 5:03
4."What's Going On" (Marvin Gaye) – 4:53
5."Passive" (Tapeworm) – 4:09
6."Gimmie Gimmie Gimmie" (Black Flag) – 2:18
7."People Are People" (Depeche Mode) – 3:43
8."Freedom of Choice" (Devo) – 2:59
9."Let's Have a War" (Fear) – 3:28
10."Counting Bodies Like Sheep to the Rhythm of the War Drums" – 5:36
11."When the Levee Breaks" (Memphis Minnie and Kansas Joe McCoy; Led Zeppelin) – 5:55
12."Fiddle and the Drum" (Joni Mitchell) – 3:06

2004 – Amotion Bonus CD

1 Judith (Renholder Mix) Stereo 4:24
2 3 Libras (Feel My Ice Dub Mix) Stereo 4:28b
3 The Outsider (Apocalypse Mix) Stereo 5:28
4 Weak And Powerless (Tilling My Grave Mix) Stereo 3:05
5 The Outsider (Frosted Yogurt Mix) Stereo 4:07
6 Blue (Bird Shake Mix) Stereo 3:57
7 3 Libras (All Main Courses Mix) Stereo 7:17
8 The Hollow (Constantly Consuming Mix) Stereo 3:40
9 The Hollow (The Bunk Mix)

2009 - Deep Cuts

1. Sleeping Beauty (Acoustic) (Live In Philly)
2. Magdalena (Live)
3. Brena (Live)
4. Orestes (Demo)