Half-Life uses skeletal animation ... 3D Studio MAX is their (Valve's) preferred modelling tool. The models have specific dimensions as per the underlying skeleton. The bones are created using Character Studio, then applied to the model. The Halflife SDK has more info about all this. It is a very involved technique and is not at all easy for newbies.
But if you are interested, try out a free skeletal animation library called Cal3D at Sourceforge.Net ... it might be of some help.
Simple 3D Vertex Animation is easier to implement and quite decent looking. (Apparently, Quake III still uses that method ... although it must be more advanced than the one I'll describe here). Looks good though, doesn't it?
Basically, Vertex animation is based on the 2D Sprite methodology. Have a frame for every move you want your character to make. Have a base model, then each successive frame, just store the vertex locations...voila...frames galore!
Best of Luck!