A set of recompiled programs that hide the activities of someone who has hacked and taken over your system. The programs would include such things s "ps", "netstat", "who", etc. on Unix systems and their analogs on Windows.
There are root kit "sniffers" that attempt to find signs that such compromises have occured, and daemons that attempt to watch for someone instaling such a kit.
A really good root kit would of course consider what these sorts of programs would be looking for and cover itself appropriately, but there are practical limits to how complicated anyone would make this. For example, one "popular" root kit forgot to modify "lsof" and can be detected through that: http://www.sans.org/y2k/t0rn.htm, and many will return different output than the "real" command would.
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