IMO, mencoder offers most, if not all the encoding options you'd ever need for your particular codec choice. Just read the man page for it, in particular in the -lavc and -lavcopts sections. I wrote a GUI for the XviD section of mencoder a while back, and it only lacks Saving/Loading settings support. Besides, with the current GUIs, one more really isn't needed, when I think about it further. :)