The best reference is the datasheets for either the mega8 or mega168 whichever flavor your using. Those can be a bear to read through but they are the best source for how the chips work and what things are called.
Another helpful source is the header files used by gcc. If you are using a mega8 I suggest keeping a printout of iom8.h, if using mega168 than it would be iomx8.h These files define the ports, pins, and most other names that are useful.
They can be located in arduino-0007\tools\avr\avr\include
Hope this helps.
Walt