Hi Mike,
my first question is why do you want to build an arduino on your own?
-Is it for size reasons (want to build sth. on arduino and leave it assembeld...too much stuff on an prebuild board unused?).
-You want to learn how a microcontroller works through that?
-You just want to try to build it?
I think there are eagle files for all Arduinos on the HP under Hardware.
http://arduino.cc/en/Main/HardwareIt's all there
If you don't have eagle installed you can use a non-commercial private version for free (they offer as download). Otherwise just have a look on the Schematics there. They are fairly easy to read and you could check what's needed to keep the bare chip running.
If you want to build a full Arduino just to use it... I think you are really better off buying one. You need PCB's, parts and so on.
I think you could use an Arduino UNO, slim it down and build with preinstalled chip, and an external FTDI cable like that one from Sparkfun if my brain has understood the basics right. You may check one of the Mini's or the Fio then. They are programmed with an external FTDI cable and I think they are quite low level of components to get it running (but SMD, so you may need an adapter board or so if you want a breadboard use of the chip alone)
http://arduino.cc/en/uploads/Main/arduino_mini_schematic04.pdf