What about the system and user tabs under "cleaning", how often do you clean the apps cache using OnyX?
As Király noted, there's not much of a need to ever do this. About the only time you would is if you lost power, the Mac completely froze up somehow, etc. In such cases a cache file may have been being written to when it conked out. A damaged/incomplete cache will cause weird issues which the OS or app it belongs to may not be able to fix. Then it would be a good idea to clear them. Otherwise, you're pretty much just wasting your time as cache files change all the time in normal use anyway.
If the space is going anywhere, I would suspect the logs. They will keep growing as you use your Mac. In earlier versions of OS X, the script cleaning tools would run at 2 A.M. (or something like that). But only of course if your Mac was on. Since most users turn their computer off, or let them sleep overnight (the scripts won't run during sleep mode, either), then the scripts never ran and the logs would get huge.
Apple changed the setup for that so if the normally scheduled time to rotate the logs was missed, they would run in the background when they could. Which means
most of the time, this should happen anyway, without you even being aware of it. Still, you could try manually running the scripts from OnyX and see how much space you recover. There's no harm at all in doing this any time you want.
As I mentioned above, though, you can clear all the caches if you want, the OS and the apps which use/maintain them will just rebuild them. It will take a day or two for the speed to come back up from a roughly 10-15% drop in performance. A negligible difference, really. And like any cache file, they are all
temporary information as caches are always in flux. So removing them entirely only slows things down a bit for a short time.