ATMEL Mega1284P evaluation board avalible

Don't know, wouldn't be bad.
ATMega1284 <$6 at Mouser.
10 boards ~$25 from itead studio
caps, resistors, leds in the pennies each range.
ft232rl $4.50
headers, shop around
power connector, crystal, can be had from dipmicro.com like 30 cents each
regulators are like 65 cents

Put in DIP cause that's the part that usually get smoked! Also folks can do development, programming, pull it out & build into standalone item.
X3 lets FT232 be used to bitbang a bootloader into the part
http://www.geocities.jp/arduino_diecimila/bootloader/index_en.html
Can likely be left off with wide availabilty of AVR programmers such as
http://www.mdfly.com/index.php?main_page=product_info&cPath=5&products_id=415

Looks like plenty of room that thruhole parts could be used for many parts instead, make assembly easier.
FTDI chip only available as SMD.
The Rx/Tx LEDs are driven by the FTDI chip, user does not have control there.
I've often thought of just leaving the FTDI chip & part off and gluing a part like this onto the board instead,
http://www.ebay.com/itm/USB-2-0-TTL-UART-6PIN-Module-Serial-Converter-CP2102-/290643946254?pt=LH_DefaultDomain_0&hash=item43abbaab0e
(Hey look at that, right from Boston too)
that would lower the cost as well.