Sure: if you put an extra-dimentional space inside another extra-dimentional space the contents will be lost and you may be going on a trip to the astral plane. Putting a Bag of Holding inside another Bag of Holding, or a BoH inside a Portable Hole for example. However, you can safely take an extra-dimentional space into a temporary extra- (or non-, take your pick) dimentional space that is created by a spell.
... and looking for it, I'll be damned now that I can't find the friggin reference. I know I've read it somewhere, and frustratingly enough I can't find it right now.
uh, little help?
Heh, honestly, until I can actually back this up with some citation, just assume I'm on crack and don't listen to me.
Edit: additional. Aha, there we go. 3.0 FAQ, pg 33.
Will extradimentional items rupture a bag of holding? The Dungeon Master's Guide says that a bag of holding placed within a portable hole tears a rift to the Astral Plane. Bag and hole alike are then sucked into the void and forever lost. The Dungeon Master's Guide also says that when a portable hole is placed within a bag of holding, it opens a gate to the Astral Plane. The hole, the bag, and any creatures within a 10-foot radius are drawn there, destroying the portable hole and bag of holding in the process. However, the descripton for Heward's handy haversack makes no mention of any rifts or gates. This implies that only the combination of a bag of holding and portable hole forms a rift or gate. Thus a bag of holding could be placed inside another bag of holding with no unusual effects.
It's a general rule that you can't mix items containing nondimention or extradimentional spaces (things that are bigger inside than out) with each other or with portable holes. Such combinatons tend to strain the fabric of the cosmos. Putting one bag of holding within another is just like putting the bag into a portable hole. Items that function like bags of holding, such as Heward's handy haversacks, cause the same mishaps when mishandled.
Note you can freely go plane hopping with portable holes, bags of holding, and the like. Spells that produce their own extradimention spaces such as rope trick, pose no danger to occupants who may be using portable holes, bags of holding and the like.