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The CPU is already done. The OpenRISC has been around for a while and is silicon proven [1].

Not quite an FPGA, but around 2001 Reinoud designed a "Meta FPGA" (the MPGA). This was essentially an FPGA implemented on an FPGA. Whilst not really practical, it was a demonstration of how one might get away from a proprietary tool chain, the idea being that the MPGA would be placed and routed once, then open source tools could place and route the user's design on the MPGA.

An FPGA would be an excellent candidate for a first "open source" chip. A keen university student could fabricate it via MOSIS [2], a service that provides cheap/free fabrication to Universities. The main stumbling block, from an open source point of view, is that many of the process specific libraries are locked up under layers of IP. One day desktop manufacturing might be feasible, especially if carbon (nanotube) based chips can be made to work and can be fabricated at low temperatures using self-assembly techniques.

[1] http://opencores.org/or1k/Main_Page

[2] http://www.mosis.com/

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Edit: It turns out that OpenCores is currently attempting to crowdfund a SoC Computer/CPU, based on the OpenRisc.

http://opencores.org/donation

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