Damn hard subject to kick off with and a bit beyond my common knowledge but I'll give it a shot
Rootkits and alternative data streams are a field unto their own requiring specialised tools such as Gmer, RootRevealer and Icesword to see them, and even then some rootkits can still hide their presence.
Some AV's can detect malicious rootkits and there are also specialised tools for detecting such.
F-Secure's Blacklight is one with a couple of others around as well.
Googling "alternative data streams" brings up a few good sites.