From my personal use with both, Dark Dynamix is considerably faster, offers far more features, is much easier to develop with, is based on an industry standard physics engine (PhysX) and is also continuing to be supported and developed whereas I remember reading that Newton (or at least the wrapper) is being discontinued.
I have the paid version so I'm not sure how limited the free version is, but from the look of the post where you can download it (
http://forum.thegamecreators.com/?m=forum_view&b=8&t=187776&p=0) you can still do quite a lot with it. However, buying it for £38 (
http://www.thegamecreators.com/?m=view_product&id=2318) if you can afford it is a good price in my opinion for the best of the options offered by Phaelax.
Dark Physics - This is basically just an old, dodgy, hard to use version of Dark Dynamix.
Box 2D - As the name suggests this is only good for 2D and your post specifically requested 3D. Otherwise a very nice plugin though.
Newton Wrapper - I used this for years before Dark Dynamix came out but it lags behind now in efficiency, features and ease of use.
XenoPhysics (Havok Wrapper) - I have not tried this myself but it is based on Havok, the other industry standard. Having read through the thread, this may prove to be an excellent alternative in time, but I'd be wary of using it in a project whilst it is still in mid-development. I'll be keeping an eye on it though.
Quick ODE - I've very little experience with this but if I'm correct in assuming that it is the semi-implemented and unsupported physics engine that ships with DBPro then I'd avoid it.
I think the best thing you can do is to structure your code so that changing physics engine doesn't affect most of your code so that you can swap physics engines around without causing yourself problems. Then maybe start off with one of the free plugins and see how you get on. If it meets your needs then fantastic. If not, then take a look at another one and see if it fills the gaps and hopefully, because of your well structure code, you'll be able to integrate it very quickly.
Anyway, these are just my views on the physics engine side of things, so please don't take them as gospel. Work out what it is you need from your physics engine and match it up against the descriptions provided in the relevant forum threads to see which ones will cover your requirements.
Hope this helps a bit!
[Edit]Fixed some formatting issues and a misplaced bracket.[/Edit]

Previously TEH_CODERER.