Dispel magic is the simplest solution for getting a wizard out of his rope-trick cause extra-dimensional space [from here on bubble], if that works in the world you play in. The RAW here is ambiguous1 but if it doesn't work, there are lots of alternatives, that I'll list shortly.
It is by no means unbeatable, if you know where it is, how to look for it or to look for it at all. - However rarely are these criteria met against the player, so they can rest in very dangerous places because no one knows either to look for them at all or how to find them. It makes perfect ingame sense, but can have side effects such as shifting the power balance towards casters and classes that rely on resting for their limited use abilities. These things can be addressed ingame too, such as by making ingame-time related plots, so they can't rest for 8 hours after every room they enter - or by simply choosing not to use it that way. If it does become a problem, modifying or banning it is an option. Two solutions are provided at the end.
- Prevention works if you suspect a wizard might try that to get away. Stop it by using dimensional anchor to keep the wizard from leaving this plane for 1 minute per caster level. Alternatively hindering the spell casting (silence, enough pain to cause concentration checks, etc.) or the movement to keep him from reaching the bubble will work.
Note that while he still has to climb (or fly) up to the bubble's entrance, once he's in he can start to pull up the rope into the bubble. And only 1 person at a time is allowed on the rope, so if he's climbing to follow him you'll get on quickly after he reaches the top.
Do you know where the hole is?
Yes - Skip to the next section.
Not exactly - but you know that it's close? Use detect magic to find
the entrance. Although it is invisible to the naked eye it's still
magic, thus detectable.
Not at all* - If you know at least who you're looking for can use divination spells that reaches beyond the material plane. Scrying for example works, but the target gets +5 to will save when in a different plane, though you can make it much easier if you have some object of theirs or part of their body. Other than that nothing works short of running around using detect magic every 60 feet.
If you know where the hole is:
Wait. It will end after the number of hours equal to his caster level, so if all else fails you can and you have the patience wait until it ends and everything including the caster will fall out. Note that if it's longer than the time it takes for him to rest he'll likely fall out with battle appropriate spells memorized.
Visit the other side. If you can climb or fly after him, assuming that he's alone in there you can chase after him with up to 7 of your buddies (6 if he pulled up the rope), one at a time.
Use explosives. Neither magic nor area effects can cross the dimensions, but projectiles can. However you won't be able to see where he is from the material plane. If the rope is still out (or not) and you have something grenade like, climb (or fly) near the entrance and throw it in, and you won't be harmed despite being near the entrance, as long as it explodes inside and doesn't fall back out first. Alternatively if you can't get near build a rocket of sorts and launch it right under the hole.
A note on making the bubble unavailable
If players use this spell in a way that takes away from the game's enjoyment (e.g. leading to an underchallenged party and less thrill because the casters are well rested at all times, or makes non-spellcasters irrelevant) you could change the way the spell works (such as having limits on how often or long for it can be used per time interval) or take it out of the game. Some decisions are made for outgame reasons only and that's okay, but if you want to include a fluff reason in the game you can just make something up.
For example: The next time the wizard uses the rope trick, the rope rises as it did before, but at the top is a little note. If you try to climb by it you knock your head as though there was something barring the room from the other side. The document reads somewhat like the kind of legal notice you get when your service is cancelled because of something someone did (neither claiming nor denying that it was you). Perhaps along the lines of "This free service is temporarily unavailable, please report error to plane administrator [and in fine print] The premium membership for SSSS (super sweet storage space) expired 2 milenia 4 centuries and 3 decades ago, thus shifting to the free SS version kindly provided by "Too infinity and beyond Inc." as per terms and conditions of use, which the plane administrator read and agreed to. Inappropriate behavior coming from your plane of existence has been reported, including trespassing and loitering thus violating the fair use clause of the terms and conditions of service for the free SS. See section IV.9.c. paragraph 2. Until further notice entrance is closed. For upgrading to premium membership, and getting the SSSS for a sweet deal of only 51 Planecoins for a limited time, contact us at one of the offices, during our opening hours. Sincerely, 2I&B Inc."
- KRyan said "By strict RAW, you cannot target dispel rope trick unless you manage to dispel the rope, which you can’t do from outside if the rope is inside. This is stupid and should be houseruled to make the extra-dimensional space and window into Effects of the spell, that can be dispelled." In this view even using Greater Dispel Magic doesn't work, as it's an effect (rope) not area spell, and as area effects (including dispel) don't travel through the window. Conceptually if you replace window with hole that makes some sense, as without anything left behind on the material plans how would dispel work? However the "hole" can be detected using detect magic, so something must be on the material side. And no area effect can pass through from either direction so it's not just a hole but a filter of sorts. The decision for balance favors allowing either dispel to work, because rope trick is only a 2nd level spell. For a discussion of use in the similar D&D3.5 system see here. I'd recommend allowing it for balance reasons, especially if detect magic is cast first.