3-D integration is going to become more and more popular in the next few years. I created a thermal cost function for a 3-D FPGA Place and Route last year for 6.374. Prof. Chandrakasan, who taught 6.374, has been researching a 3-D FPGA. I haven't done any further work on it since the class, but I read an article today about integrated cooling which made me think about it again (I've looked into implementing the thermal FEA on an FPGA, but others have already done similar things). Xilinx is certainly interested in this research. FPGAs have implicit fault-tolerance which means that yield issues associated with 3-D integration can be marginalized (in fact, Xilinx sells their "defective" units as application specific devices).
The remainder of this blog entry was written on 7/19/05.
3-D chips require less wires. As shown in this thesis and paper, 56% less interconnect is required for a 5 layer chip. Wafer bonding has been thoroughly investigated, and processes compatible with standard CMOS are being refined. Tezzaron is using this technology for memory.
The big problems facing the industry are the lack of good design tools and the issues associated with yield and heat. Design tools will be developed as the processes become more refined. Yield issues and heat need to be taken into consideration in the design. Consider if you have an 80% yield on each wafer; when you have 5 layers of silicon--assuming defects are not correlated to the location on the chip, and no defects due to the bonding process--your yield reduces to 33%. Of course, we are able to have more redundancy with more silicon layers, so we can design systems that are fault tolerant (google: fault tolerant architectures. lots of good stuff). The costs of the chips will probably directly represent the decrease in yield -- good designs and tools will save companies a lot of money (though i shouldn't give away my secrets before i patent them :-)
Cooling higher density chips is the major hurdle towards development of 3-D circuits. A few documents hint that microfluidic cooling systems may be the solution. Georgia Tech researchers made an advance on this end a few weeks ago by presenting a microfluidic manufacturing process compatible with standard CMOS
Expect lots of great things in the years to come. For now I expect 3-D integration to creep into specialty mixed signal chips that are extremely expensive, and memory where heat generation is less of a problem. Microfluidic cooling technologies will be adopted in the near term for 2-D high power chips. The first 3-D micro-processor architectures will probably use extra layers for clock distribution, global interconnect systems, and power distribution systems. Caching systems will likely be added as a third layer until new design approaches (and better tools) allow for the design of multi-layer integration with logic interspersed between the layers.