Can a GPS waypoint be used when filing a VFR flight plan? This probably equally applies to IFR flight plans, but the general question is can arbitrary (unrelated to an airway or named fix) GPS coordinates be used in the route on a flight plan?
Yes, nothing prevents you from doing so, and it is quite common.

Flying VFR does not require you to actually navigate by means of visual reference, it just requires you to remain VMC in accordance with the airspace class you are in.