I have just cleaned my Mac Pro. Yes you are on the right track. I pulled out the processor assembly at the bottom, the SuperDrive tray at the top (both very easy), and the graphics card (at little bit harder), and with compressed air in one hand, and vacuum cleaner in the other, I blowed and vacuumed out all the dust, there was heaps!
As others have suggested, use the compress air conservatively and in brief bursts, and only when the vacuum can't get to or dislodge some dust. I've had one graphics card fail due to the build up of dust in his fan fins, so I recommend getting it out and cleaning those little fins - which will probably be clogged with dust.
My Mac Pro now runs much quieter, and happier I suspect.
Old thread, but this might help others.
I had my Mac Pro suddenly refuse to recognise one of the riser cards for memory. As it had been an extremely hot spell recently, and the MP runs 24/7 and it has done through hot spells in new, I suspected a build up of dust or the memory or card just needing re-seated.
Re-seating did the trick, but there was a lot of dust inside.
So I used my camping air pump, 240v with a variety of nozzles. I attached a not too thin nozzle, and borrowed the rubber hose that is part of the stethoscope in my child's doctors kit, attached it to the end of the nozzle. I removed everything I could from inside the MP and then blew the dust out from the inside, out through the cheese-grater mesh. Pens were put through all the fans to prevent them spinning while the pump was active.
Has anyone else done something similar with other "household" items ?
CAUTION: Do not use a household vacuum cleaner near your important electronic equipment. The plastic tools can generate large static charges that can kill electronics long before you feel the Zap of a static discharge.
If compressed air seems too messy, move your Mac to a place where dust is a don't care, such as a garage or outside.
There is not threat whatsoever of moving dust INTO awkward places that might impact electrical performance. Component engineers routinely talk of connectors making a "gas-tight" connection. The only threat is spinning your Mac's fans so crazy fast that they might be damaged, and a little moderation is all that is required to avoid that problem.