Skype vs VoIP?
Sorry to be a nit-pick - Skype is VoIP. I think you mean:
Skype versus SIP (integrated with WM6) or
Skype versus H323
I'm not sure of the nitty-gritty of Skype, but most of the VoIP I've seen uses standard codecs over a real-time channel, usually using UDP e.g. G711, G723, G729, GSM etc. The difference here is the control plane i.e. SIP is text based markup versus Skype which is proprietary.
Personally I think the integrated SIP client in WM6 sucks. Its nice in the fact that its integrated with the dialler, but the support for G711 only/jump through hoops to get the provisioning working makes it a last resort for me. Counterpath has a good SIP client that even supports GSM, G729 but its a standalone app and not integrated into the phone.
My $0.02