After long hours of googling at work and at home, I finally arrived at http://www.excaliburtech.net/archives/192, stating this is the way to disable IPv6 autoconfiguration, say when you’re more keen on using a manually configured IPv6 address:
netsh interface ipv6 set interface "Local Area Connection" routerdiscovery=disabled
While you’re at it, you might want to disable Teredo, ISATAP, and 6to4:
netsh interface ipv6 set teredo disabled netsh interface ipv6 isatap set state disabled netsh interface ipv6 6to4 set state disabled
Afterwards you can simply use the GUI and set your desired IPv6 address, its prefix length, your default gateway, and your DNS server’s IPv6 addresses. The same recipe applies even to Vista and anything onwards.
It’s a bit surprising not to find any article on MS TechNet describing this setup, but maybe the keywords I fed to Google were a bit off.
(Microsoft Windows Server 2003 (R2) isn’t as mature as 2008 (R2) and 2012 (R2), and in the case of manually assigning IPv6 addresses on 2003, you must simply accept the fact that the automatically generated IPv6 address can’t be removed at all.)