650D case is a great case if done properly. First off as mentioned, upgrade the front intake fan. Coolermaster megaflow or Bitfenix are popular upgrades. Personally I use a 200MM NZXT for the highter CFM (160+) and I just deal with the added noise.
Also you should consider totally removing the hard drive racks and mounting your drives in the upper optical drive bays. This will give the intake charge a clear path to the mobo and graphics card.
The H100i is a solid option, one I use myself to great effect. One thing you may want to do is have the H100i fans pull in cool air from the outside. This will bring cooler air across that radiator and also help contribute to positive case pressure. They wont cause any heat issues to the mobo by blowing in towards it. I wire the fans to run off the mobo fan headers and control them that way. this keeps added cables out of the CPU area and avoided extra software
Positive case pressure helps prevent dust from being drawn in through all the seems, cracks and vents in the case. Even with running filters a large amount of dust can be brought in this way. With positive pressure, as long as you have higher CFM of air being pushed in than your exhaust fan you are good. I have the 120 AF series on the back of my 650D for exhaust, the CPU cooler and front fan as intakes
Filtration. The stock filter in the front is a joke. Demciflex makes awesome filters that fit the 650 top. They make a standard round 200mm that you can use in the front. this will keep things very very clean.
Here is a pic of my rid for example. also many fine examples on the 650D case forum. Hopefully this will give you airflow and lay out ideas.Edited by badkarma3059 - 3/31/13 at 3:22am