How do I find out what version Protocol specification is describing?
As of october 2013, the protocol version is 70001. It's not linked anymore to client versions (so it doesn't correspond to version 0.7.0.1 in particular; 70001 was introduced in 0.8.0), and is intended to go up in increments of one, as changes specified in BIPs are implemented.
There's now a good overview at https://bitcoin.org/en/developer-reference#protocol-versions. The latest as of March 2014 is 70002.
The latest protocol version can be found by looking at the latest canonical Bitcoin client implementation source code currently v0.8.5 at https://github.com/bitcoin/bitcoin/blob/v0.8.5/src/version.h#L28. This should tally with what is described at https://en.bitcoin.it/wiki/Protocol_specification.