Some things that comes to mind:
*Fast/Technical/Wanky solos. A bit ironic seeing how I loved DT a few years ago, but I guess the table turned. I can appreciate a good solo, but it's very off putting for me when it's all about displaying technical skill. Or cramming a solo in there just for the sake of it. I don't like the idea of having a guitar solo, followed by a keyboard solo (and then maybe another instrumental part) and suddenly you have 4-5 minutes of instrumental stuff that doesn't fit into the song at all. In terms of solo's I much prefer feel and passion over playing fast. (and before someone tries to argue that fast solos can have passion, I didn't say that they couldn't)
*Hidden tracks. Like pointed out earlier, it just bothers me when there's a 20 minute song that has 4-5 minutes of music in the beginning, and then 30 seconds of mumbling at the end. I don't really come across many of these, but the few ones I know are slightly annoying. Luckily it's always on the last track, so I can always stop after the real song is finished.
*Long songs for the sake of being long. This is semi-related to my first point, but a very common part for some Progressive bands. I can appreciate a good long song, but I think the length has to be justified. There are loads of long songs where I feel that the original sound or idea gets lost along the way, and that the final product isn't that interesting.
A few bad examples that comes to mind: The Ministry of Lost Souls by DT, and Celestial Elixir by Haken. I'm not saying that these are bad songs (and it's fine if other people like them), but for me they are both very long songs, and very scattered. I've heard both several times but can't seem to recall exactly how they sound, maybe a section here or there, but somewhere along the way I feel like they get out of hand, and loose focus.
On the contrary I think two good examples would be Six Degrees of Inner Turbulence by DT and Raider II by Steven Wilson. The first to show that I think DT can write good stuff as well, in this case I think despite the long length it holds up very well. There are recurring themes but the individual songs are just as interesting as the whole thing. (if you count it as a song or a song-cycle is another question), and as for Raider II, I think it's a song that follows a red thread without becoming repetitive.