Intake fans are kind of useless now

Both AMD and Intel recommend an exhaust fan directly on the level of the CPU to take care of the heat generated by both AGP card and CPU.

An easier solution is to take rubber spacers, glue them onto the side panel and mount an old power supply fan so that it blows sideways onto CPU and AGP. The space provided by the rubber suffices in most cases to get enough air moving. Alternatively, you can drill a few holes into the case.