I've got a couple each of the NKC and Fundamental Logic serial boards, and 5 of the RBBBs. I use the former when I'm doing something with a shield, and the latter when I'm not. I treat the RBBBs like big chips: I plug them into a protoboard with whatever other circuity I need for the project, because that tends to be cheaper than buying a prototyping shield.
The only significant difference is that most of the "official" Arduinos have a USB interface on the board. Which is more convenient for most folks. Especially when they're using the Arduino as a PC peripheral. Since I'm also a cheapskate when it comes to PCs, all my development systems are old enough to have "legacy" serial ports. Plus I often do projects that interface to serial devices. So it's more convenient for me to have a serial interface and a power supply that doesn't depend on being plugged into a USB port.
It's pretty much a matter of taste, and of what sort of things you're doing with the Arduino. If you're only buying one or two Arduinos, and are a typical user, you'll probably prefer to buy them ready-made. If you have a good parts supply on-hand, and don't mind trading some time for a few dollars' savings per board, go for the bare Freeduino boards.
Yes, I've also kind of been thinking along those lines too. But if I do buy a mega, it'll probably be a clone, because they're usually so much cheaper :P.