So one can't really tie the ground of a circuit with a 7905 back into the ground of say.... your USB peripherals? I don't get that. Figure 7 of the Fairchild LM7905 specs show a circuit where the ground is tied into a 78** series.
You can, as long as that's the ONLY connection (remember, it's all relative, and "ground" is arbitrary). So, if you're using a floating (i.e. isolated from everything, which is a common design) wall wart to power the 7905 circuit, you can happily hook the resulting "ground" up to USB/PC "ground" (which, remember, is also tied to Earth via the 3rd prong on your AC cable as well as to the metal components of the case, and some wall warts do the same).
However, if you're using 12V from your PC supply, you have a problem as there's already a connection, and you've redefined the meaning of "ground" when building your 79xx positive regulator circuit. The same goes if you've already established any other connection between your circuit and the PC prior to defining the "ground" node.
Notice that the application circuit in Fairchild's datasheet for using a 78xx in a negative voltage application shows a transformer on the input. I would hazard a guess that's probably to illustrate this fact.
You could in fact use 2x 7905 (or 7805) to create a +/- 5V dual supply with a common ground node, but you'd need two supplies that are isolated from each other to start with if you want to continue the notion of common ground throughout the circuit. If you use a 7805/7905 pair, then you can get by with a single split supply (e.g. +/- 15V) on the input while keeping the same ground reference.
The 7905/7805 pair gets around this by flipping part of the topology around so that the ground reference is continuous throughout the circuit. Rather than regulating "ground", it regulates the "output", which is more along the lines of what you expect and can probably wrap your head around.
In a nutshell, to save your sanity, use 79xx for negative voltages and 78xx for positive voltages
