I've been using visualhub for a while now and apart from my HD movie files I have converted all my TV shows and Movies, about 1TB in total.
I use iTunes tab > Apple TV ? H.264 > Go Nuts
problem is my 350mb episodes ended up at aroubnd 600mb and my 1.07GB 720p eps ended up over 4 gig in size!
so all I do is hid the advanced tab and "Limit video size to" and set the size to my original file size.
means I get Apple TV compatible video, in full quality, in the same file sizes as i'm used to and happy with.
I've also been using Xgrid (Mac Pro and Macbook pro) this is converting them SO much faster, I can convert a 350mb TV episode in less than 4 minutes.