#1 is a nylon standoff that you can use for holes where you run out of the brass standoffs that you'd normally use to screwdown the motherboard, or for places that it's hard to reach a screwdriver into. You don't want to use them in a spot that gets any up or down force during mounting of memory or adapters, since that will result in the board flexing. The corner behind the PS/2 ports is usually the hardest spot to fit a screwdriver, and is a safe place for that. Of course, real standoffs and screws is the best.
I dunno what #2 is meant for. Only recently have I seen that sort of longer screw coming with cases. I've never run into any need for them. Maybe they're meant for optional feet or something.
#3 are the brass standoffs -- screw those into the holes in the case motherboard tray, in the holes that align with the holes on your motherboard (only the holes with a silvery foil around them are meant for screws). These may use either a coarse or fine-threaded screw to mount, I've seen both types -- you can just test each one with a screw to make sure they go in easily but not too loosely, as the fine-thread screws are usually slightly smaller. If you have both, try to use all the same type in the system so there's no mixup.
The brass standoffs also don't need to be used if your motherboard tray has an integrated standoff, like a pillar either molded into the tray, or snapped in. Yours probably doesn't, but you may get one like that in the future, so just remember it.
#4 is kind of hard to make out; you probably have 2 or 3 different types actually in that pile, because that's an awful lot of screws.
The screws for securing case side panels are usually a coarse thread, with a knurled (kinda wavy) underside to the head, which is hexagonal as well as having a phillips cut. Those are also used for securing PCI/AGP cards. The knurls on the head help to keep them from loosening. There may also be a similar type but with a smooth underside on the head. Those can usually be used to secure the motherboard. The smooth surface won't scrape off the foil around the motherboard holes. You may also find some non-hexagonal headed screws with a smooth underside and coarse thread; those can be used for the motherboard as well.
Hard drives also use a coarse thread screw. You can use the same knurled screws used for the case panels or PCI slots, since they'll help to prevent any loosening due to vibration.
Optical drives and floppy drives use a fine-thread screw. You may have some with a hexagonal head, and some with a rounded head. They're pretty much inter-changeable -- just test a few in the drives first; they should go in easily but not feel loose, like you could just pull them straight out. The black #5 screws may in fact be those screws, just colored black to differentiate them.
