Reading through the thread, I notice a reoccuring complaint that 'such and such is not allowed for by the rules'.
This is simply bunk. Just about everything is allowed for in the rules. The limitation is not what is allowed by the rules, but what is allowed by the rules for an entity of a given ability.
Leaping tall buildings in a single bound is allowed by the rules. Leaping tall buildings in a single bound with only a +3 bonus to your jump skill is not.
There's no precedence for this in the rules; even if you create a spell called even more deeperer darkness that can suppress daylight, something like a miracle or disjunction should be able to light it up.
Maybe. Maybe not. Something like a miracle or a disjunction ought to be able to effect anything which is the result of a 9th level spell effect. But 9th level spell effects are not the limit of what the rules allow. If
Even More Deeper Darkness is the result of Epic spell casting, or the result of the divine ability of a being with at least 1 divine rank, then there is every reason to think that a mere wish or miracle might only have a marginal effect or a chance to work, or - depending on what entity is behind
Even More Deeper Darkness - no chance at all. Wishes and even miracles are not the absolute limit of power in the game. What I would object to however is a villain with 12th level spell casting ability creating some effect which the DM by fiat claims resists even a wish or miracle simply because the DM doesn't want the PC to use that resource to overcome the problem. In such cases, a spell casting PC has every right to complain, "Why can't I do that?"
If you don't want the PC's using thier resources to overcome the problem, you shouldn't give them to them. It's generally only fun to negate PC resources when they have so many resources that overcoming things by brute force is beginning to get dull for them. If your PC's have thier ability to fly removed by DM fiat (its a epic effect, its an alternate plane, whatever), and there is a certain new excitement and fear mixed into thier play that you haven't seen in a few levels, then you've pulled that trick from your big DM bag of tricks at the right time. If you are doing it because you have an antagonistic relationship with your PC's, and you can't turn PC resources against them with the same creativity that they have, maybe you should step from behind the screen for a while.
Lastly, there is in 3rd edition never any reason for old skool 1st edition absolute claims like, "nothing can harm the widget" or "no force can resist the irresitable object". Any 3rd edition designer worth his salt, wishing to enforce his puzzle or challenge and take away the obvious short cut need only set the DC of solving the challenge in that fashion above what is reasonable for a character of that level to solve. For example, DC's 30 or more above effective character level are impervious to all but the most narrowly created specialists. A hardness of 30 or more and a decent amount of hit points will prove immune to the brute efforts of all but very high level characters, especially with other defences in place to discourage that approach (for example, a level shocking grasp is triggered whenever the object is damaged, and the object has 50 such charges). You want a door that always shuts? Instead of saying, "It always shuts and no force can stop it", point out that it is a gargantuan object and has an effective strength of 60.
The important thing is to grant that the characters could duplicate such challenges had they equivalent resources as the challenges creator. The world should not work one way for the PC's and another for the NPC's. So long as it works in the same fashion for everyone, it's not cheating.