I think every good engineer has a little box or two full of loose parts. You know, you take a few from a cut strip, fiddle with them, and then just never bother to put them back. It's not always easy to put them back in the strip anyway. It's not such a big deal for passives and inexpensive parts. When you need something assembled, you just buy another strip of ten (or however many you need) for $0.29.
We sometimes can assemble from loose parts, but it's never a good idea. They can be dirty, damaged or of mixed value. It takes us extra labor time too and we'll probably have to charge for that. Since we're using robots to assemble, we'll have to put all of those loose parts into an empty strip. Ugh. Components manufacturers don't want you to store your parts loose either. They know that having the things rattle around can cause damage or contamination.
But when it comes to the bigger, more expensive parts like BGAs or QFPs and things, it can be more of an issue. Still, though, your ultimate goal is a sold, reliable piece of hardware. If the QFP ended up with some pins bent (as in this picture) or the BGA had some balls drop off, you've probably lost your goal no matter what. So keep those expensive parts in their original packaging.
When you look at the total system cost, a new part or two probably doesn't seem so expensive anyway. A Freescale MCIMX31LVKN5B processor in a 457 ball BGA is only $26.00 from Digi-key. Getting a new one of those is pretty cheap compared to the risk of spending a week trying to diagnose a problem caused by a BGA ball that cracked because of poor storage.
There are some processors, FPGAs and other specialized components that can cost hundreds or even thousands of dollars each. Those parts are probably worth repair if pins are bent or balls are knocked loose, but the best bet is to keep them in their original, not extra crispy, packaging.
We don't have 11 herbs and spices in our solder paste