Actually there IS no change, maybe you misunderstood the making of Runaway the same way I did. You are right - the Runaway characters were constructed in 3d and rendered with cel shading, BUT they are PRE-rendered in the game (with a a really high amount of frames per animation), it's no real-time 3D rendering.
(Yes, I am sure about this - now! ;-) !)
So finally Runaway uses the same methods as you are used to. The shadows are possible due to alpha channels, Brassfire already mentioned. To reach your goal, you have to construct your character animations in e.g. 3ds max 5 (which has a built-in cel-shader!) and use the rendered frames as you are used to in your 2d environment.
Ok, I was confused. I was hoping to avoid all that lengthy importing of every frame.
Did you need to import your shadows seperately from the character?
Do you know how WME handles the resizing of the character then if it's not true 3d?
Oh - what game did you release, something we can have a look at ?
Well, about two years ago I released Pizza Quest ... if you google it you might find it on the net I abandoned the website long ago.
Right now I'm wrapping up the production of a very large classic VGA 320x200 game, which you can see here:
http://socko.adventuredevelopers.com I've always wanted to make a classic Lucasarts/Sierra game, which AGS is perfect for. But my next game I want to be 800x600 or above like Runaway ... with like I said 3d characters and 2d backgrounds. With WME and a few more art classes maybe I can do just that.