Here are a few links to tools & libraries that I find useful.

Arduino

Arduino IDE Download
Adding support for other chips

Atmel ATtiny Datasheets

ATtiny13A
ATtiny25/45/85
ATtiny2313

Atmel Mega Datasheets

ATmega8
ATMega48/88/168/328

Eagle

Eagle is the tool I use to design PCBs
Eagle Download Site
Adafruit Eagle library
Sparkfun Eagle libraries
Eagle library for headers
Eagle library for SMD headers

Other Chips

NXP PCF8563P – Real Time Clock (RTC)