The corporate market has moved to VOIP at an amazing pace in the last few years. Apple and most of their telecom partners have relaxed the rules recently allowing VOIP calls over 3G. However the VOIP user experience on the iPhone is still very poor. I have been using Skype, Fring, Viber and various SIP clients like Acrobits Softphone and Groundwire -- probably the best SIP clients out there. While the cost savings can be significant, the lack of proper iOS integration means that those tools remain immature. Here are some of the shortcomings:

1. Bluetooth support is not always implemented. When it is the behaviour is different in the VOIP client and the default dialer (e.g. you cannot control the VOIP dialer from the handset). 
2. If you receive a POTS call while on a VOIP call, the call will be put on hold right away. You are not given the option to reject the incoming call or tell your current correspondent to hold on. This is actually a show stopper for serious use. This is an iOS feature that cannot be overidden. 
3. Receiving calls is still hit and miss. Some clients use background processing, some use notifications. Neither method is ideal. Again missing hooks in the OS make implementation difficult. 
4. Putting the phone on silent does not put the VOIP client on silent. I am not sure if all clients are affected but I suspect again, that this is due to the OS failing to expose the proper API. Acrobits clients do exhibit this issue and this is a serious one: when you receive a call you have no way of silencing it!
5. Lastly while the iPhone usually does a good job and moving from 3G to WIFI the other way round just does not work. It means that if you are on a call on WIFI and move away from the hotspot, you will  lose the connection.