I've learned a lot about this problem, lots of little things. First of all, if the fan blade is close to the holes in the sheet metal, it will cause sheering turbulance of air comming in, making a terrible noise. This usually affects intake fans when the sheet metal is flat, or nearly flat. That's part of the reason many cases have a raised grill area in front of the fan, rather than a flat one.
If the holes are too small, it makes a whistling noise. Of course 1000 little wistles sound more like a turbine engine than a wistle.
There's one more thing that makes fans louder: Harmonic resonance. That's one reason I usually tell people to get thick steel cases.
OK, tacking the problems: I've actually cut out fan grills to get rid of the noise associated with the holes being to small or too close to the blades. Spacers help if the holes aren't very much too small and are simply too close to the blades.
The best way I can think of to isolate the fan from the panel to reduce resonance is to use gromets. If you can find sheet metal gromets with 1/8" to 3/16" holes, you can drill the mounting holes larger to fit the gromets, and install the fan against the gromets by putting a screw through the hole.
Of course that moves the fan away from the panel allowing it to suck inside air in from the sides. You can fix that with duct tape. Really! You can even buy black duct tape.
Where to find rubber gromets? Good question! Auto parts stores might have them. They're generally used to feed wires through sheet metal panels.
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