I'm in the final stages of downloading the blockchain, and I've noticed a copy of the peers are using software that appears to be out of the normal sequence. One is Satoshi 0.11.99 .and the other is Bitcoin XT 0.11. Are these non-standard nodes? and should I worry about them?
Satoshi 0.11.99 is just a build of the next version, 0.12. The next version is never bumped up to its actual number until a little bit before actual release. Anytime you see a Satoshi x.xx.99, it is simply a version that was built from the source code and has not yet been released.
Bitcoin XT is just another client. It is a fork of Bitcoin Core.
You do not need to worry about those nodes.