It would be interesting to know the rationale for the rules.
For the R&R queue area, I'm willing to bet that it is a contractual agreement (or lack thereof) with Aerosmith. For dark rides, I assume that it is for the enjoyment of other guests. For backstage areas, I assume that it is to protect the mystique and to control information about changes.
Why one ToT and not the other? Why was it not OK for Nemo and now it is? Why was it OK for CoP and now it is not? Why allow flash at FotLK (where there are guests directly across from you) but not at other shows? Why allow flash but not video lights at FotLK?
BTW, Disney security has been known to stop and question photographers about their intentions with no real reason. I've been questioned simply because I was carrying an extra lens and a few other items. They didn't do anything but ask a few questions (no waterboarding). Who knows what they'll do if you look Middle Eastern or Midwestern or whatever the flavor of the day is.
Has anyone heard of anyone getting in trouble for anything photography related at WDW? At the Nemo show under the old rules, I saw several people quietly admonished, but nothing on the order of forced deletion, expulsion, etc was ever done.
Ok, I will try to answer all of these to the best of my ability......
R&R - I doubt there is a lack of a contract there, I would bet that if anything the new contracts says no, but my guess is that more than likely it is the same reason as on COP (see below).
Dark Rides - It is due to the fact that the lighting is part of the show and the flash ruins the effect (I have indeed seen some people escorted out of the park for taking flash pictures on POTC at DL).
DL TOT - Because at least one of the effects can be altered or ruined by a camera, WDW doesn't have the same effect (I will not post which one fore those that may not have been to DL).
Nemo - When it first opened there were certain contractual issues with the performers that prevented photography, they have since renegotiated those contracts (Note "Professional" equipment is still not allowed and some people with such equipment may be asked not to used it during the show, this includes Tripods, Digital SLRs and the like).
CoP - The official rule is no flash photography, but a lot of times if there are too many people or the CM doesn't want to have to sort it out afterwards they say no photography period, so every time that they only mention no flash photography, I take full advantage of it.
Monster's Inc. - No photography in the attraction or que (this one is due to copyright issues with Pixar, although I am surprised this hasn't been worked out by now).
FOTLK - No video lighting as it interferes with the carefully planned theatrical lighting and can blind the performers. The theatrical lighting has been set up in such a way that it minimizes the impact of the flashes on the performers and the guests across from you and a brief flash doesn't bother the performers as they have it happening all the time, usually when no flash is allowed it is not so much for the performer's safety as it is for the comfort of those around you and to no interfere with carefully planned lighting).
I have never been questioned by security, but I have been asked not to use a tripod at Snow White (at DL) and one time I was taking pictures at Aladdin (at DCA) in the box seat on the mezzanine, and the CM by the door kept pacing back and forth, I finally turned around and asked her not to do so as it was distracting to us watching the show, she then told me to stop taking flash pictures (my flash was off the entire time and the lead confirmed this when I talked to her as she was in Orchestra directly opposite of where I was at and would have seen, it should be noted that the lead took us over to TOT and we got to go in on the FP side, this was at a time when the standby was over 2 hours, so that was very nice indeed). I have only had one problem at WDW and that was at Monster's Inc., the CM said no flash pictures were allowed inside the auditorium (I know, because I listened very carefully as I know some Pixar attractions are particular about what you can and can not take) and then I was told no pictures at all, I protested but lost the battle.
Also from time to time there are exceptions, for example I went to Who Wants to Be a Millionaire play it during star wars weekend once and they had a special show before hand that they did allow photographs during, so always listen for what the current rules are and when in doubt, just ask.