Most security tools have had IPv6 compatibility built in for years. For example, see nmap’s multitude of IPv6 options. With nmap6 being launched yesterday, it’s even more clear that nmap is much more than a vulnerability scanner.
Nessus has supported IPv6 since version 3.2, which was out in 2007.
Similarly, Metasploit has had it since 2007 (version 3.1), though it took a few months for payloads, stagers, etc. to catch up.
I haven’t used w3af in a long time, but it also had IPv6 support and since it’s part of Rapid 7, it obviously links in very well with Metasploit (as does nmap).
I don’t play much with code analysis tools, but as far as I know there are no compatibility issues for most.
You’ll obviously have to change your scripts from IPv4 addresses to IPv6 so there’ll be some tedious work there as you check things and validate that everything still works, but in terms of the tools actually working, the compatibility with IPv6 is built in for most of them.