I'm about to write my first '3d' game, and I'm wondering if you would recommend me to use a scene graph? The game isn't really 3d, but it will use MDX for rendering, and probably models for characters (at least to begin with). I also think I want to use bone based animations and possibly later on ragdoll physics. The game is tilebased (basicly square tiles with a texture id and height), and the camera will be fixed from above. There'll be a couple of races, and all of them should be able to do the same actions (fighting with sword, with mace/club, with bow, and they should be able to climb, jump and swim as well). So, scenegraph or is there something else that might be better?

I think scenegraph is just a data structure or object structure, it really doesnt matter if your games is a 2d or 3d, u'll definitely need some dynamic structure to hold all the entities and update them during game play.

Scene graph is just a readymade one which has all the node type for what ever entity u imagine in your game.

Most engines have it , either knowingly or unknowingly...

eg: check out openscenegraph , it has a hierarchy of nodes and varioustype of nodes to suit any 3d entity... but only limited to representing 3d data..

irrlicht games engine doesnt reffer to any scenegraph, but for each entity u need to put on the scene u create a node (already defined) or define it yourself , and insert it to a parent node.There are lot many types of nodes here...

In the end what u always end up getting is something like a scene graph,more of a
directed acyclic graph(DS) sometimes also a tree.

Then there are various algorithms to visit each node during game play and update them.