| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Junklantis | 2 | 43 | Saturday April 3, 2004 |
| Lap of the Gods | 5 | 105 | Saturday February 16, 2008 |
| Legend of the Five Dragons | 5 | 107 | Saturday March 1, 2008 |
| Lone Raph and Cub | 1 | 24 | Saturday October 18, 2003 |
| Meet Casey Jones | 1 | 4 | Saturday March 1, 2003 |
| Membership Drive | 5 | 110 | Saturday March 24, 2007 |
| Milk Run | 6 | 134 | Saturday April 14, 2007 |
| Mission of Gravity | 3 | 67 | Saturday February 5, 2005 |
| Modern Love - The Return of Nano | 2 | 37 | Saturday February 21, 2004 |
| More Worlds Than One | 5 | 108 | Saturday March 8, 2008 |
| Nano | 1 | 5 | Saturday March 8, 2003 |
| New Blood | 3 | 65 | Saturday January 22, 2005 |
| New World Order (1) | 5 | 111 | Saturday March 29, 2008 |
| New World Order (2) | 5 | 112 | Saturday April 5, 2008 |
| Night of Sh'Okanabo! | 6 | 123 | Saturday October 21, 2006 |
| Nobody's Fool | 3 | 62 | Saturday December 11, 2004 |
| Notes from the Underground (1) | 1 | 13 | Saturday May 10, 2003 |
| Notes from the Underground (2) | 1 | 14 | Saturday May 17, 2003 |
| Notes from the Underground (3) | 1 | 15 | Saturday May 24, 2003 |
| Obsolete | 6 | 118 | Saturday August 5, 2006 |
| Outbreak | 4 | 95 | Saturday February 18, 2006 |
| Past Present | 5 | 114 | Saturday April 19, 2008 |
| Playtime's Over | 6 | 121 | Saturday October 7, 2006 |
| Prodigal Son | 4 | 94 | Saturday February 11, 2006 |
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