I thought Walking with Dinosaurs collection to be fascinating with some neet-o-keen animation and CGI to keep kids interested as well as being educational. And I'm in my 30s There are two different versions out, the oringal one that I have and a more expensive full set collection...
It's only Dolby Digital 2.0 though so no 5.1 surround track on it.. but it's still cool!
Both of those came to mind right away. I haven't seen Dinosaur, the animated movie, but unless I hear it's really bad, I'll probably get that. Thanks for the warning about it being scary - my little guy doesn't seem too scared of anything so far, but we'll see.
I rented Walking with Dinosaurs a couple years before I had a kid and loved it myself, so maybe I'll pick that up as well.
Though the series isn't factual, have you considered The Land Before Time? This is a series of [how many now?] feature length animated movies about a group of young dinosaurs, and how they survived a drought by banding together to get to "the great valley," after being separated from their parents. At least the first one is.