29'r refers to a mountain bike that runs over sized tyres on 700c rims which have a diameter of 622 mm and they draw their name from the wheel and tyres they use.

The 700c designation comes from the French and once denoted a 622mm road wheel that accepted a narrow tyre... there was once 700a, 700b, and 700d sizes but these are now obsolete and referred to medium, wide, and wider rims that accepted wider tyres.

The 26 inch tyre designation is probably the most confusing as there are many wheels / tyres labelled as 26 by X although the most common is the 559mm wheel/tyre that is used on modern mountain bikes that will come labelled 26 by x where x is a decimal.

Sheldon's article on wheel sizing pretty much covers it all and the system of using the ISO / BSD is by far the best way to confirm that a given tyre will fit a given rim.