IPv6 runs over the same lower-layer networking (such as Ethernet) as IPv4, and the transport protocols (TCP, UDP...) which run over IPv4 also run over IPv6. This means that most IP-based applications can run over IPv6 with little modification.
Domain name service (DNS) works for IPv6 addresses along with IPv4 addresses, so names like www.uiowa.edu & whois.arin.net don't change. What changes is behind the scenes, where in addition to the "A" records for IPv4 addresses, there will be "AAAA" records for IPv6 addresses.
Services (web pages, email, domain name service, remote login...) can run over IPv6 alongside IPv4. Making an existing service available via IPv6 is usually not disruptive to its IPv4 availability. Applications individually choose which protocol to use, often unbeknownst to the person using the application. For example, the Firefox web browser will use IPv6 if it's available for the URL requested, but will use IPv4 if not. Other applications might prefer IPv4, but can be told to use IPv6.
Most current user systems do the right thing regarding IPv6, including:
- Apple OS X
- Microsoft Windows Vista, Windows 7, & Windows 2008
Most older versions of systems are simply not aware of IPv6, so they don't pose a problem. However, there is a chance that a system is aware of IPv6 but doesn't do the right thing, which might require disabling IPv6 on that system or upgrading it.