The Nemesis queue sounds great! From the descriptions given, it sounds like it's the best.
I loved the Dueling Dragons queue, but we never had to wait in it - I would imagine it would get old pretty quickly. When I'm waiting in line, good theming just doesn't do anything for me. After you stare at the same thing for a while, it ceases to be interesting (down with all of the indoor queues (FoF, Mr. Freeze, many Batmans, etc.). For that reason, I like the Mantis queue line because of the view you have of the ride. The RB at SFGAm is also pretty good (although those ummm..."roofs" can get in the way of your view of the ride).
I must take issue with the Batman queue. Although I haven't been on the Batman at SFMM, every Batman (not just B:TR) queue I've been in has been exceedingly annoying. They've had blaring, obnoxious sound effects, corny announcements, and much more.