I came across this excellent guide yesterday. It might help explain a lot to those new to W3 Total Cache.
http://zemalf.com/1443/w3-total-cache/ - I recommend checking out the e-book zemalf has on scribd. The link is on this page.
Additionally this post helped to explain opcode caching and setup APC. http://www.virtualmin.com/node/15258#comment-69432
BTW I've implemented nearly everything in W3 Total cache and my site went from a 63 to a 94 in YSlow. Not to mention about 600-700ms on load time.