Agreed, it looks like 2D animation of pre-rendered 3D graphics.
You need to work with a lot of animated layers to get that, including 2D skeletal animation (if you study Flash animation you'll learn all this). The special effects can be done in After Effects as mentioned.
I do not think they look weird. Very impressive work to say the least.
EDIT: After seeing the rest of them I changed my mind; I wouldn't be surprised if most of the material to be animated through 2D rigging was painted by hand instead of modelled and rendered. There's just too much detail in some characters - it's much cheaper to paint all the separable layers by hand (which is not hard at all if you know what you're doing), and animate them with 2d rigs according to how the composition was planned.
A simpler 3D model of the character (like the ingame one) would serve to render the character in pose to use as a guide for correct perspective and how to break on layers, then the artist would paint the final version by hand based on this reference.
Of special note is the shading of some elements. Whoever did this really knew their After Effects.
Notice the leg of the creature on the right side of the screen, it has a reflection effect.
[media]http://www.youtube.com/watch?list=PL3B1F171F3009BE74&feature=player_detailpage&v=OTBfu9-nhuY[/media]