For IPv6 we support TCP scanning (connect()-style), host discovery (connect) style), version detection, and NSE in Nmap. So you have the basics. Also, pretty much every part of Ncat should support IPv6 (there might be some aspects which don't due to lack of testing, but we'd consider that a bug to be quickly fixed). Ndiff supports IPv6 too.
However, Nmap cannot do the raw packet IPv6 stuff, such as UDP scan or the raw-packet TCP port scans (SYN, FIN, etc.) or raw packet host discovery modes. I agree that it would be great to add that functionality, and we're always looking for volunteers!