Yup. As R.G. says, you'll need a 68mm (English-threaded) BB shell, but other than that you need whatever spindle lengths your new cranks require. You've noticed that different versions of Shimano 105 square-taper cranks (I assume both are double cranksets - it would have helped if you'd specified in your post) require different BB spindle lengths for correct chainline.
ISIS is more straightforward - nearly all ISIS cranks are built to the same standard, so road doubles ideally go with 108mm, road triples with 113, and off-road triples with 118mm (b/c off-road rear hubs are 5mm wider). I'm not sure about Octalink.
But jur pointed you toward Sheldon's BB-length database, which should take care of you here.
I don't actually think that it's worth your changing to an ISIS crank, though, unless you've got a good deal on one and one of your current cranks needs replacing. Square-taper spindles are slightly less stiff, in a way that's basically unnoticeable by the vast majority of riders. Square-taper sealed-cartridge BB's also have a much better record for durability than splined BB's, because the larger BB spindle in the latter leaves less room for bearings, meaning the bearings are smaller and subsequently less durable.
If you want more of an answer, say more about your situation.