Hardware wise, the schematics are available but not under an open source license (commercial use prohibited), as far as I know PCB layouts aren't. Not sure about the case.
Software wise, the closed source parts are the OMAP boot ROM (virtually unavoidable), WiFi module firmware, PowerVR libraries and firmware if using 3D, modem firmware (but there is a switch to kill modem power) and eventually (not in the current OS) audio offload DSP firmware.