Agreed on lots mentioned here. Odd time signatures, etc. Also, try your hardest to make music that no one else but musicians listen to. That way you play for 20 years, then finally gain commercial success when you put out your 'Shredding 101' DVD.
Seriously, though. Do your best to avoid songs that just sound like a bunch of parts strung together in order of playing difficulty. Music like this can get really tedious after a while. Ask even the most die-hard Dream Theater fan. They've all hit the Fast Forward Button many times. And if they say they haven't, they're lying.
Listen to bands like Porcupine Tree, Riverside, etc. They are considered 'progressive rock' bands, but IMO their music is very 'listenable,' especially to non-musicians. For the harder stuff, there's always Mastodon, Tool, etc. Lots of hooks and memorable parts in that stuff. And check out Kansas. A lot of their songs have multiple parts, but they all seem to 'fit' together flawlessly and lend themselves to the overall cohesiveness of the songs.
AVOID, let me repeat . . . AVOID guitar-driven prog rock like the plague. I can tell a guitard-ruled prog rock band from a mile away. B O R I N G ! ! Go back to Berkeley and impress your friends, Mr. Shredomatic!! I want to listen to MUSIC, not get a lesson in chord theory or arpeggios.
Listen closely to Symphony X. Yes, Mike Romeo can shred his a__ off, but Symphony X is NOT a guitard band. Their music is of a whole. All the parts fit nicely together, and nothing is thrown in just to 'mix things up' or make it more technical. The neo-classical thing is nothing new, but Symphony X does it extremely well. IMO, they're probably the best neo-classical metal/prog band out there. And Romeo is certainly no stranger to the memorable riff or hook.
Another thing to avoid is doing an extreme metal/prog type thing ala Between the Buried and Me or something like that. There's way too much of it in metal-land, and it's getting old really fast.
But then again . . . do what you want to do. If it works for you, then go for it.
BTW - IMO, playing in odd time signatures really helps one's timing in a universal sense. I often write in odd time signatures, and laugh when run-of-the-mill hard rock/metal or indie types glaze over into a stupor because they've never played in 7/8 or 5/8.