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.

Arduino comparison

Characteristic Sanguino Arduino Arduino Mega Leonardo
Processor atmega644P atmega328 atmega1280 atmega32U4
GPIO Pins 32 20 54 26
Analog Pins 8 6 16 12
PWM Pins 6 6 14 8
Flash Memory 64K 32K 128K 32K
RAM 4096 bytes 2048 bytes 8192 bytes 3072 bytes
EEPROM 2048 bytes 1024 bytes 4096 bytes 1024 bytes
External Interrupts 3 2 32 13
JTAG yes no yes yes
I2C yes yes yes yes
SPI yes yes yes 2
USARTs 2 1 4 1
Onboard USB<->Serial Converter? no yes yes in-chip