The host segments were what originally drew me into the show (specifically Hugh Beaumont revealing himself to be of the Four Horsemen in Lost Continent), so they've always been my favorite part of the show.  To be honest, some of that was probably because the riffing just wasn't as good back then. 

But I'm going to guess if I'd discovered the show later one, I wouldn't have nearly the fondness for the host segments.  I've gotten my wife into the show over the years, but she can't stand the host segments and greatly prefers Rifftrax to MST3K.