Most of these have been mentioned in this thread, but to summarise the DT instrumental that I know about (and some of them might be considered a stretch), we have:
- Black Clouds & Silver Linings collectors edition (missing keyboard and guitar leads though)
- A Dramatic Turn of Events deluxe edition (solos intact)
- The Enemy Inside (Japanese edition of Dream Theater)
There's also a quite a few demos that are still in instrumental form:
- Train of Though demos Ytsejam release (slightly different solos)
- Under A Glass Moon instrumental demo (before James' vocals were added)
- Learning to Live instrumental demo (ditto)
- Take The Time instrumental demo (ditto)
- Metropolis instrumental demo (ditto)
- Scarred instrumental (Bonus track on The Awake demos, known as "Keymaster")
- Home (early Live rehearsal of entire first half of song)
- The Spirit Carries On (another live rehearsal of the instrumentation, from "The Making of Scenes" bootleg)
- When Dream and Day Unite early production instrumental demos
- There's instrumental versions of some Majesty tracks like Another Won, Two Far, Your Majesty (I only mention these for curiosities sake, probably not what the OP was looking for)
There's also instrumental versions of these songs floating around the internet due to their appearances in Guitar Hero and Rock Band and the stems being accessible:
- Pull Me Under (extended ending kinda, nothing to get excited about)
- Constant Motion (instrumental version is based on the guitar stem so is missing the keyboard tracks)
- Panic Attack (Also missing the keyboard tracks)
- On The Backs of Angels
And then as mentioned previously, there's Jammit. Awesome stuff in there, bit overpriced. Still, very cool that it even exists.