Skype is a type of VoIP, so a better differentiation is whether to go for a Skype-based solution or use something like an Open Source Asterisk or commercial VoIP system.
For general one-to-one calling with a few other telephony features, Skype will do the trick, but if you want traditional PBX-type features such as:
- Inter-site transfers by extension
- Comprehensive voicemail
- Out of hours call handling
- Call parking
- Ring groups
- Hunt groups
- Hot desking
- Operator functions
- Busy lamps
- Call routing by rules
Then a 'proper' (sorry, Skype) VoIP solution is the way to go. You can always bridge Skype to, say, Asterisk, to get the best of both worlds too.
Edit: If you don't fancy running and managing your own VoIP system, you can have a hosted solution - the key phrase here is 'voip centrex solutions'