bigger surface area means better connection but.. adapters add extra points of contact so using adapter is always worse than original connector.
so.. for computer usage, I would just use 3.5 to 3.5.
In theory, if distance from computer to your headset is quite long, like ten meters, then using thicker cable and 6.3mm connector on headset end and adapter to connect it to computer might get some benefit.
in short, it's about impedance, which affects sound volume, not really quality. dirty/bad connectors can affect sound quality though.
Edit: as can bad quality cabling, which becomes more apparent the longer they are but.. again, for desktop usage, not really an issue.