Seafoam Green
Fender Strat that has a removed pickup selecter switch taken out. It also has regular abalone dot inlays. It was used during the Enema of the State period.
Blue
Fender Strat that has had a white Invader, but then switched to a black one.
Chrome Silver
Fender Strat that probably has taken the most abuse, if you look at the dents. Many times, this guitar was used to capo up to F#, but was also used to play songs in standard tuning.
Red
Fender Strat that is tuned down 1 1/2 steps. I don't think it is a Sub-Sonic, although it might be and he just got a different headstock. It has 22 frets, unlike his other guitars.
Teal Green Metallic
Fender Strat with an Atticus heart sticker by the bridge.
Orange
Fender Strat with abalone dot inlays.
Natural w/ black racing stripe
Fender Strat with a black racing stripe, Ash body, Masonic inlays, no pickguard, and a Les Paul mounting ring holding the black Invader in place.
Black
Fender strat with white Atticus sticker by the bridge. This was and still is Tom's favorite guitar, but it was smashed at the 2001 EMA's because of a short in the guitar. It is no longer being played as a result.