Try using a plastic card (debit, credit card) to squeeze the major bubbles out and let the little ones sit a few days and hope that that they "cure". Think of it as window tint, right after its done, there are still bubbles in the tint, but they cure after a few days and disappear
If you are looking for a good screen protector, go for the Apple crystal film or the anti glare. They are easy to apply and look and feel really good. If you are willing to go through the process, i HIGHLY recommend the Bestskinsever film, its 10 dollars for the full body skin. They have a nice replacement policy, but make sure you keep your order number because they will request it when asking for a replacement. Its just like Invisible Sheild, but you don't have to pay anything, no shipping. So you get 2 full sets for the cost of 10 dollars.
+1 for the screen protectors that are sold through Apple. They're called Power Support. I have the crystal ones on both my V1 and 3G. I tried these Casemate ones through the AT&T store and they were awful. (that was just a convenience thing-one stop shopping) Went through a few that made awful bubbling that looked almost like it ruined the screen! Then finally the last one was okay, but started to curl up. Decided to replace them with tried & true, and the 3G looks great now. Luckily I was in the direction of the Apple Store, so I picked them up, but would have ordered just as easily!
crystal film is the best. i've been wanting one for some time, but always get busy the last minute or go to the store and they're sold out. and also, i want the new black marware sport grip for the 3G but the Apple store is ALWAYS sold out when i go
RATHER depressing if you ask me. i want to and probably will order one online though i just hate knowing that i cant get one at my local Apple store =/