I prefer 3 3/4, primarily due to space issues. I also like that vehicles and playsets can be reasonably priced and scaled for these figures.
6" is nice too though. I love the Marvel Legends and the current release of Batman. The articulation sucks on the Batman figs relative to the ML stuff though. And McFarlane sportspicks, aliens, predator are in the quote/unquote 6" scale. The predator figures dwarf the ML stuff, so not quite the same scale. The hockey figs look so much better in that scale and with that detail than did the older stuff.
12" does little for me. I have a few and they look cool on display, but they leave so much opportunity for error and it becomes glaring when it happens (Hoth Han first release). The imperials look nice though, no faces to sculpt.
As with others, thank goodness LOTR didn't do 3 3/4, I would have been in for sure. 6" takes too much room for those.