Several thoughts:
- Buy quieter fans. Quiet and bleeding-edge performance usually don't go hand-in-hand. Lower your overclocks (if any) and buy fans in the ~1200-1400 RPM range with bearings that are known to be quiet.
- Suspend mechanical hard drives. Vibrations can echo throughout your aluminum or steel case, and can be avoided by using some sort of soft material (even rubber bands) to mount hard drive instead.
- Switch to a SSD for your OS drive. Even with a quiet case and a soft-mounted hard drive, you'll still hear a mechanical hard drive clicking away as it reads and writes. SSDs make literally no noise, and having the most accessed drive in your system completely silent can make a huge difference in overall noise level.
- Buy a different case. Older cases that use primarily 80mm fans can be replaced with a good, newer case using 120mm (or bigger) fans for less than $60. Larger fans move more air for a given amount of noise created, meaning that if things are already cooled well with 80mm fans, you can get away with even slower (and thus less noisy) 120mm fans.
- Got a tower-style CPU heatsink? Go fanless. If your case has an intake or exhaust fan right next to your Megahalems / TRUE / V8 / Hyper 212+ / Venomous X / etc. and you're not running a serious overclock, you can take the fan(s) right off of the heatsink for a bit less noise overall.
- Buy a power supply with a good, quiet fan. Something like the Antec Signature series or Seasonic X series / Corsair AX series should do well.
- Hearing annoying vibrations from inside your case? Try tightening down all of the screws you can find. If that doesn't work, try packing different areas with tissue paper or paper towels and see if you can get it to stop. If you can, you may want to add some padding material (foam / rubber) on those panel(s).