I tried AVSMedia, but you know how it is. It doesn't work like I'm used to, so I went back to my trusty old Nero Vision.
What I was hoping to do was create personalized menus, but turns out it's a bit too much work for my taste, and Nero Vision had a somewhat suitable template. So I just create chapter points on the videos, and I was all set.
It's still encoding as we speak (I'm having the encoding done on the oldest computer I have, which never gets used anymore, yet is still a 2.1 Ghz Athlon XP, so it's still decent)