You're knda rght - 32bit OS's can only address around 3GB RAM, but that's not to say that rest rest is all wasted. As pointed out in another thread (today?) the higher registers of your RAM are allocated for system hardware use, so your actual 'wasted' RAM may be as little as 256MB. This is especially the case if you use on-board graphics, rather than a dedicated card.
The reason that a lot of manufacturers put 4GB RAM in is for economics. It can easliy work out cheaper to put in 2x2GB sticks than it is to put in 2x1GB + 2x0.5GB to give 3GB.
Using 4 RAM sticks also limits motherboard choice for the manufacturer, as only having 2 DIMM slots is not uncommon.