How to detect whether your machine is compromised?

[Raj Kiran Grandhi <grajkiran@gmail.com>]

Hi,

There is an article on slashdot,
http://it.slashdot.org/article.pl?sid=07/10/05/1234217&from=rss which 
says that most of the phishing sites are being run from rootkitted linux 
boxes. I dunno how accurate their analysis is (the results were not 
released), however I wonder if there is any way to establish whether a 
given machine is compromised or not.

Are there any tools available that one can run on a regular basis? What 
measures can we take to ensure that we are somehow alerted if our system 
gets compromised?

Regards,
Raj Kiran