One I discovered recently: Part of the main keyboard theme in Lifting Shadows Off a Dream (first heard 35 seconds in) reminds me of the main keyboard riff to Love Will Tear Us Apart by Joy Division, both is terms of melody and instrument tone. Not exactly a typical Dream Theater influence, but given the overall mood and tone of Space-Dye Vest, I wouldn't be surprised that Kevin Moore was listening to some Joy Division at the time.
On a more abstract level, Learning to Live reminds me of Heart of the Sunrise for some reason. There's nothing musically that sounds alike, but the songs have a similar lengths and both serve at their respective albums closing epics, and both songs contrast quiet, contemplative vocal sections with sections of aggressive prog instrumentation. There's also some similarity in the imagery used in the lyrics: i.e. "Listening to the city, whispering its violence, I set out watching from above" & "I get lost in the city", and both songs have an overall "warm" vibe to them. For all these reasons I mentally connect the two songs. In fact, you could go further and say Images & Words is DT's version of Fragile, with Pull Me Under as their Roundabout (an 8-minute album opener that's still prog but was catchy and mainstream sounding enough to be edited for radio airplay, and became a hit single).