Currently Being ModeratedJul 9, 2012 11:29 AM (in response to ureshii)
There are two kinds of hidden files, one OS X uses to store info it needs without a user deleting them, this you don't want to do obviously.
However for privacy reasons there are cache files you can delete, use the #12 OnyX routine here for that.
Also according to what your describing you have been Emptying Trash, thus the files are still on the hard drive waiting to be overwritten with new data.
Now you realize that and want to "scrub" the free space on the hard drive, so after you use OnyX and reboot, then you use Disk Utility > Erase Free Space option (Zero erase or 7x overwrite) on your Macintosh HD partition. Takes awhile (7x even longer) because all available free space is addressed to secure erase)
You can read more about it here
You only need to Secure Empty Trash on files you don't want to ever be recovered from a hard drive, if you set it all the time, it gets to be a pain as it takes so long as it's using the 7x overwrite function.
If you have a SSD, you can't delete or scrub the drive, as you will read in the last link.