I know that on a 6 pin PCI-X power connector the spec says pin 2 can be disconnected. It is another 12v pin like pins 1 & 3. If my graphics card only requires a 5 pin connector, is it still safe to use a 6 pin?
There's no such thing as a 5 pin PCIe connector (pci-x is totally different from PCIe and is hardly used. Its PCI-extended, not PCI express) - there's 6 and 8 pin connectors, and the middle '12v' connector is optional in 6 pin connectors - see the pinout for a 6 pin connector here. It should be entirely safe.
Triple 12V connections on 6 pin PCIe seems to be for compatibility with 8 pin power connectors, which must have 3 12V inputs, and is often supplied as a 6+2 pin connector. The extra 12V is ignored in that case.