When we designed the Freeduino boards, we made 100each of the 4 candidate designs, and they all worked in preliminary testing.
The through-hole version was developed further, eventually being sold in kit form by NKCElectronics. ( http://store.nkcelectronics.com/freeduino-arduino-diecimila-compatible-board-complete-kit.html
(and also now by Seeed: http://www.seeedstudio.com/depot/freeduino-usb-complete-kit-p-58.html?cPath=6_7
That PCB version is something like 1.19.2, and you can find it here: https://docs.google.com/file/d/0B6dMB5dovDUZNGRlMmRhMTItYjUwZC00YTY5LTgwMTYtYzU1NmU1NDQyMTQy/edit
(It has an "edit history" layer, so most of the changes are documented (and cosmetic.)) (Note that there was substantial wishy-washiness WRT the voltage regulators, which affects the layout relatively substantially.)
Note that this design was based on the Arduino Diecimilla, and is substantially outdated by this time. No power-switching circuitry (though you might think that a feature!), no "R3" connectors, no avr usb controller, wimpy 3.3V power, etc.) Furthermore, most of the politics that led to the desire to develop this board was resolved in favorable ways, so that to a large extent the freeduino board is no longer necessary.
(in fact, the timing was such that it wasn't really necessary by the time it was done. It's current claim to fame is it's "kit" status.)
(Likewise, I've contemplated a "v 2.0" Freeduino board, "cost reduced", but that's not necessary either.) (and alas, one of the major ways to achieve cost reduction is to go all SMT...)