Things like timer registers, pin definitions... true/false - whatever - there should be a master, printable reference PDF somewhere
Well, all the Atmel-defined symbols (timer registers, for instance) should get defined via the <io.h> include that is part of gcc. The chip datasheet is probably the reference for those. The m328 has about 100 registers, each of which has individual names for most of its individual bits (because you know PORTA4 might somehow have a different value than PORTB4), so a full listing is probably going to be too cluttered to be useful.
arduino.h is going to have most of the arduino-specific values; there are a lot less of those.