Atmel's documentation is usually clear, well formatted, sufficiently redundant (similar sections are often near copy-paste -- saves on time having to read through different sections), and well enough explain the code or registers or logic or whatever. They do lack in the implementation / detailed / analog department though. Example: the crappy ADC, BOD and POR in the ATmega series, and good luck finding any guaranteed min/max parameters on them (even a lot of typ are missing).
Also the same sorts of things from Altera: good luck finding I/O pin characteristics, power supply specs (bypassing, current consumption..), that sort of thing.
Tim