I'm in the camp that says players should be allowed (even encouraged) to use their higher-level abilities, but they should realize that the bad guys will too, and no one spell or ability can solve every problem.
Rope Trick: Recently the heroes in my campaign had dire wolves from an evil temple hunting them. Rope trick didn't protect them from being tracked or scryed upon, allowing their opponents to set up a couple of ambushes. Even better, one of the enemy spellcasters used a rope trick to hide in near the ambush, waited for the party to become fully engaged, then exited the rope trick invisibly and started lobbing fireballs! Later, when he fled (the party defeated their attackers), he flew away invisibly and the party spent several hours near the rope trick, waiting for him to come out. They're still not certain he wasn't in there the whole time - they just know they didn't catch him.
Teleport: Some GM's don't use the failure chances, which makes this spell far too powerful. With the chance of failure, a party won't use this for every day transportation. And, as Kugar mentioned, it's very easy to create adventures which force the use of teleport, allowing the party to use this ability to save the day, not wreck the story.
Invisibility and Improved Invisibility: Whenever a character goes invisible, I don't allow the other players to automatically know his/her position. They know where the character is *supposed* to be (if they planned ahead), but without see invisible or something similar, an entire party of invisible characters is liable to trip over themselves. Also, many higher-level encounters include opponents who can find invisible foes, so these spells shouldn't be an autokill by any means. On the other hand, I strongly encourage my players to scout before charging, and using invisibility on the scout is a smart choice, IMC.
Scrying: This one's tricky. It hasn't become a problem in my campaign yet, but if it does, I see a couple of factors which will help. One, I'll make sure the players know that scrying can be detected, so they shouldn't assume whatever they see is accurate - a little paranoia should go a long way. Also, they have to know who to scry upon, and when. Not even high-level wizards can scry the same person forever, certainly not without being noticed and having their target take appropriate action. In television and movies, the heroes always happen to overhear something critical - in the game, the party wizard may spend an hour learning nothing more than what the target likes for breakfast - or he may learn of the plot to kill the king. It's up to the GM to adjudicate, based on the party's actions. Scrying should never be like looking up the answers in the back of the book, so to speak.
