Your pictures are really small so it's hard to see what you are talking about. If you can, repost using photobucket or another picture hosting site.
In general, a car manufacturer will make one wire harness for all of their models. So if your model doesn't have, let's say, a factory radio, you will still have the wires/plugs for one. I have several connectors under my dash that are factory and aren't used.
Now, if you are looking at aftermarket wiring, for say a stereo or something like that, then I would trace them down to see if they are being used. If they aren't, you can either cap them or remove the wiring all together. If they are connected directly to the battery and aren't being used, then I would remove them.