The regular Arduino has plenty of pins for most projects, but if you need a bit more, then the next step is the Atmega, with lots of pins and an SMD chip. For DIY the Atmega644 is a solution. A bit more power than the 328, but still available in DIL. It is the same chip as used in the ‘Sanguino’. 

PA0-7 are the analog ports.
PB0-7 are Digital ports 0-7
PD0-7 are Digital ports 8-15
PC0-7 are Digital ports 16-23

R3 and LED2 are the standard ‘test Led’  circuit. For compatability it should be connected to pin 19 (PD5=D13). Do this via a jumper, so the test LED can always be switched off in case you need to put something else on that pin.