There's the double row header connection which is the GPIO and there is also two rows for JTAGw
The JTAG is used for test access, hardware/firmware debugging and firmware loading - not something the average user of the board will be doing.
Pic from Wikipedia.
On the schematics
for the Rev.B, one row is used for the LAN controller, (connector P3, sheet 2, ref A4), and the other is for the CPU/GPU and is connector P2, sheet 4, ref G2.
Unless you specifically want to bang the hardware directly, there's not much point in worrying about them.
On a side note, the choices are hotting up: Raspberry Pi faces challenge from Android-based rivals