If your ideal is compressing WMVs with AME, you can do that easily - on a PC. AME on a PC gives you all the granular control you expect, but with the added encoding options for WMVs. Personally, I run a virtual machine with a minimal Windows 7 volume in VMWare Fusion, but you could use Parallels, Bootcamp, or better yet, keep a small, inexpensive PC networked to do those occasional PC-only tasks.
There's also a free tool called VideoMonkey, which is what happened to the now-abandoned Visual Hub. It will allow you to do a 2-pass encode, which is better than the stock Flip4Mac.
I highly recommend Video Monkey instead of handbrake for this type of conversion.
It has a more streamlined interface and a nice checkbox that lets you restrict the bitrate of the output to that of the input. Additionally, it will attempt to find metadata for TV shows and movies so that they show up nicely in iTunes.
It's based on the open sourced VisualHub code.