On board the AVRs that can be programmed are those in the schematic. For other members of AVR family or the rest programmable ICs that Ponyprog can program, there is the J1 connector (CON10) which allows expanding the programmer's hardware. See Ponyprog's site for other's ICs Ponyprog circuits. The JUMP1 jumper is there to connect the crystal's circuitry to the 8-pin AVRs or to disconnect it. Some AVRs have internal RC oscillator and an external XTAL is not allowed or needed.
Check the JUMP1's table and the datasheet for the AVR of your choice for more details. The JUMP2 jumper is there to allow programming a member of the AT89Sxxxx family or the AVR's AT90Sxxxx & ATmegaxxx family.