Sorry to interrupt the bitching about the UI of the website, but...
I would nominate a working familiarity with:
Non-trivial graph algorithms
Serious distributed systems design (ie. building something where anything and everything can fail at any time, possibly in nasty or even byzantine fashion)
Formal methods
Optimization methods (ILP and so on)
Binary decision diagrams
as some other "ninja arts" if we're going to have to use the term "ninja".
