First thing I did was ditch the stock CPU fan. I replaced it with a Pabst 8412 n/2gml. Airflow is ~26cfm at 19dBA. At least that's the rating. Given the stock fan is rated at 39.5 cfm at ~34dBA it seems ok. The stock fan normally did ~2/3 max speed so it's in the right ballpark.
I mounted this by knotting elastics through the holes and wrapping an elastit around the frame. This isolates it effectively. The stock mounting method makes contact with the CPU heatsink/radiator. Not good for noise. I also used rubber grommets to isolate the actual fan cage from the case. You will need longer screws for this. I cut out the stamped grill and used the stock fan wire grill on the outside of the case. Very quiet when done.
I tried using a Zalman HP80a on a Ti 4200 card. It works, but cannot fit inside the case. I eventually used a Thermaltake GF4 cooling kit. I wired 2 100 Ohm 1/2 watt resisters in parallel and used the video card's fan header. This drops the fan speed to a tolerable level and allows me to close the case. As with the PSU fan below, I connected the fan's header to the motherboard with only the yellow wire connected.
The PSU is the biggest source of heat. I ended up replacing the fan inside it with an external fan ( sunon kd1204pkb1 ). I chose this one as it pushes more air than the stock PSU fan and is quieter. ~24 dBA if I remember correctly. It's thicker than the stock fan so it won't fit inside. I mounted it on the end inside the case, just under the cables using silicone. Voiding the warranty, of course, I cut out the grill on that end and removed the stock fan ( leaving the external fan grill intact ). I used the fan wires to power the new fan and connected the new fan to the motherboard fan header ( only the yellow wire is connected ). This actually allows me to monitor the PSU fan speed. I also sealed up all the remaining vents as I am blowing air INTO the PSU and want the air and heat to go through the unit and OUTSIDE the case, not to recirculate inside.
I still need to try isolating the hard drive, and maybe enabling the Maxtor's quieter drive settings ( Diamond Max Plus 120 Gb ).
The end result is that this system is ridiculously quieter than stock. Even sitting next to its sister system with the same mods except for the PSU fan mod, it's considerably quieter.
Your major noise source in these XPCs is the PSU. You'll notice the CPU fan swap. Your video card fan will probably swamp anything else.
I also run all the fans without guards. They introduce turbulence and I have no reason to reach inside such a tiny system while it's running so I fail to see the need for them. You can't touch any of them with the case on anyway. The wire guard on the outside is necessary due to sharp edges and I don't want things bumping the heatsink/radiator assembly. The PSU fanguard should remain in place. It doesn't affect airflow in any real manner and you definitely DON'T want to accidentally reach inside when moving the unit.
Overall air temps have not changed much, if any. The CPU fan guardian feature is off. The PSU fan rarely kicks into a higher speed. Most noise is simply the hard drive. There's a definite soft whoosh airflow noise at all times but it is not unpleasant and barely noticeable.
Also, the grommet mounting of the fan cage leaves a gap. I haven't bothered to fix this as there's a definite "hot pocket" of air at the top of the case. I figure that this gap may cause some air circulation in the top of the case, but that's entirely conjecture on my part.
All of the fans and VidCard coolers I used can be found at http://www.plycon.com
Not an endorsement as such, just where I happened to find the parts I needed.