In terms of animations, Unity animates things differently than Blender. With Blender, you can create animations for your model, such as "Run", "Walk", "Idle", "Attack", and these will all be executed on a mesh-level. But the animations in Unity are primarily for animating properties on your GameObjects. If you want to animate the transform, scale, or rotation, you can. You can also even animate script variables using the Unity Animator.

So it really depends on what you want to do. If you want to create character animations for specific movements that pertain to your character, do them in Blender. If you want to create animations that affect Unity-specific variables, then use the Unity Animator.

And (I'm no expert on Ragdolls having never used one before), but I think what you do is assemble the entire thing in Blender, with a bone structure and mesh hierarchy, and then you import your mesh into Unity where you assign each sub-mesh to the Ragdoll component and Unity will create all the proper constraints and joints for you to create the "Ragdoll" effect.

Unity will import Blender's armature based animations, that is bone-based, and nothing else. There is a useful script in Blender under the Animation script menu where it will bake constraint based animations for you, ie if you have things in Blender that drive your models bones, and animate it, this script will make the much needed animation sequences that Unity can read. Failing that I think you can animate in either program effectively. I suggest watching JoeRobbins' tutorial on animation here: http://blogs.unity3d.com/2010/05/05/animation-view-video-tutorial/

In our game we use Unity's built-in animations for character movement along paths and FBX-imported animations for the actual character deformations. Just make sure you have both nested, ie. the character (w/ animation) parented to the gameobject that has the path animation.

You could use Unity's animation system for simple in-model animations like a box being cracked open and so forth. Unity animations main advantages are:

• You can re-sample your animations frame rate on the fly without any penalty - it's really a world of difference having stuff animated at 60-90 frames per second instead of 15 or 30 FPS. In the other hand, imported animations at such rates will sensibly increase in size.

• You can fire scripts at specific points of your animation, a bit like what you do in Flash, eliminating the need of guesswork or any timing logic to get, for instance, that particle effect showing up in a specific moment of the animation.

Good luck!