It also seems appropriate as every other member has an alter-ego/persona.
They recognize the memes exist, but they don't really embrace them or use them as means of self-indentification, though Jordan has done a pretty good job of flipping the "wizard" thing into a nice brand direction for himself, in a way that "pirate" or "bear" can't be flipped.
Becoming stale, annoying, and overplayed is just a natural part of an internet meme's lifespan. It's cool that the other guys in the band have acknowledged their little nicknames, since it shows that they pay attention to us, but really they were right to keep the memes at an arm's length, whereas now I can't read a JLB twitter update without rolling my eyes. I mean, shit, "pirate" is part of JLB's twitter username. It's just lame, in my opinion. I like James "as is". I don't care to constantly be reminded about a joke fans made-up years ago.
I guess I don't have anything really constructive to say about it beyond that, though, so I'll try and be good and just let everyone else enjoy the Pirate JLB meme
EDIT: Okay, I do want to say something about this:
I'm sure there are myriad of other bands that have weirder things than a nickname. For example Avenge Sevenfold with there alternate names. Not much weirder but that's what they go by. James only has a nickname, A7X has alternate identities.
Edit: Korn with the masks, Kiss with the face paint. etc..
Great point. When it comes down to it, though, Dream Theater are one of those bands who actually play to their strengths by being serious. It comes with their territory, as a progressive metal band.
When I think of Dream Theater, I think of music that's very crafted and cerebral. I think of the members of Dream Theater as students, really: each member both a master and disciple of their craft. In fact, most Dream Theater fans I know are pretty serious people, who are very diligent themselves about some craft or art or form of learning. When I rank Dream Theater albums, the ones that come out on top are the ones that incarnate the Dream Theater values of seriousness and thoughtfulness: SDOIT, I&W, Awake, SFaM, etc.
When I think of my least favorite Dream Theater albums, no surprise, it's the ones where they were just blowing off steam, fantasizing, or plain goofing off: ToT, SC, and so on.
So, in a roundabout way, what I'm getting at is that Dream Theater are serious business. That's why gimmicks have never really worked for them, despite what other metal bands have done with their naming / outfitting. In the end, the best thing about Dream Theater are those five guys: James, Jordan, Mike, and the Johns, and the way they showcase their talent and artistic expertise to create really intricate music.