/etc isnt called /conf or configuration because it contains examples, scripts and other small stuff as well, which is etcetera.
/var is for variable data like logs and pid files, not meant to be changed by the user directly
/opt sucks and is for losers who dont know about /usr/local or how to install stuff in ~
The Linux way makes much more sense than Windows or MacOSX way. binaries are in bin libraries are in lib, whats not to like?