Making your own DIY Arduino board is interesting and challenging amusement. The biggest complication is always the burning of the bootloader. Such kind of "Catch 22 : http://en.wikipedia.org/wiki/Catch-22_(logic)" acts - you can not program your board through the USB because it is not preliminary programmed. The solution is known - the board must be initially programmed through its ISP interface. You can find a lot of cheap or expensive ISP programmers in the electronics stores, Ebay, Amazon...etc, but my experience learned me that the universal relatively cheap programmer able to program wide range of AVR (or PIC) chips does not exist. I have tested USBTinyISP. It had problems with Arduino Mega (ATmega 2560), I have tested USBasp bought in Ebay. It was also not working with Arduino Mega. I updated the firmware with the last version - the same result....
I have decided to try to find some simple and very cheap programmer to try with it. My experience with the PIC chips told me that may be the best solution would be to find a circuit of serial programmer, working on the RS232 computer port. ATTENTION: This will work only on PC having real RS232 serial port. USB to RS232 adapters could not work. If the port has TTL levels - it would not work also. Searching in the Internet I found the following circuit. (Copyrights : Olimex). It is very simple and I hoped that it will be reliable.

Step 1:

The parts needed:

1 x RS232 9-pin female connector - my had plastic housing
1 x 6 or 10 pin ISP connector (depends on the type of your ISP cable)
2 x zenner diodes 5.1V
1 x diode 1N4148 or similar
1 x NPN BJT 2N2222, BC864B...or similar
2 x 10 KOhm resistors
2 x 4.7KOhm resistors
1 x 33 Kohm resistor
flat cable (6 wires)

For the assembling of the programmer I have used a piece of veroboard.
It had the metal pattern shown on the picture.

Step 2:

I decided to embed the whole programmer inside the housing of the RS232 connector. I cut a small piece of the veroboard. I shaped it by sanding. For the circle cuttings I have used a round file. The process of the manufacturing can be followed on the series of the pictures. How to connect the parts can be seen there also.

Step 3:

After assembling and inserting the board inside the RS232 housing, i filled the whole housing with hot glue to fix the parts and the cable and to prevent some short circuit caused by binding of some part pins. To connect the ISP header (connector) to the other side of the flat cable I used a very small part of the veroboard. My connector was 6-pin, but also 10-pin connector could be soldered. The pin correspondence can be seen on the picture.

Step 4: Finished!

Now the AVR ISP programmer is ready!

Step 5: Time to Test...

It is now time to test it!
I have used the "Ponyprog" software. It can be downloaded here.
I decided to try the programmer on some more simple AVR chip, instead on ATmega2560, because if a problem appears it will difficult to find what the source is - or the microcontroller, or the programmer. For the test I have used ATmega32.
How to connect the ATmega32 to program it the the ISP can be seen on the picture.
To program it I have used a breadbord with supply board.
In opposite to the USB AVR programmers, which can provide the power supply for the programmed chip, this programmer requires that the chip is supplied by an external power supply. Even more... this supply also must be connected to the "VTG" pin of the programmer.

Step 6: The Programming...

After assembling of the breadbord and supplying the chip is time to start the test.
The programmer is inserted in the RS232 port.
"Ponyprog" is started.
First the connection ports and the type of the programmer must be defined.

Step 7: Calibration ...

Calibration must be done and the type of the chip must be selected.

Step 8: Let's Try to Communicate...

Now we can try to communicate with the AVR chip. Let's read the device...
We can read also the fuses.

It works!
Now we have for less than $2 a working AVR ISP programmer which fits easy in our pockets.