Hi Slicendice, I had written a fairly long post for you but I messed something up in IE and lost it all!!!
Seeing as it's late I haven't the energy to write it all again so here is a summary which hopefully tells you all you need to know!
The DO wins hands down on portablity, the 100-400 is quite a chunky beast - I definately notice the extra size/weight in my backpack.
Build quality - nothing to choose between the two, both are beautifully made and very solid with metal bodies.
Image quality - at 400mm the 100-400 is fractionally sharper than the DO is at 300mm, there is hardly anything in it though, both are very good. The 100-400 gets a bit sharper as you back away from 400mm so it has the edge over the DO in the overlapping focal lengths. The DO has the advantage of going to 70mm on the wide end - 70mm versus 100mm doesn't sound much but it can be useful.
IS - The DO has second gen IS which is noticeabley more effective than the 1st gen IS on the 100-400 (it still works well though and is worth having).
Focusing - Both focus very quickly, quietly and accurately however the 100-400 seems to hunt more than the DO in low light.
Zoooom - I actually really like the 'controversial' push pull zoom on the 100-400, it works really well and is the ideal mechanism for a lens with this focal length. The zoom ring on the 70-300 is very heavy - you really feel like you are shifting some serious chunks of glass about!
I am already in love with the 100-400 after just 24 hours but I think it is going to have a slightly longer learning curve than any other lens I have previously owned to get the best out of it. I got the 100-400 purely for the extra length as I want to do more wildlife shooting. The DO has gone to a new home but I really wanted to be able to keep it too.
Both lenses are great, the 100-400 has the optical edge but you pay the price in size and weight. I would say on balance if you don't need the extra mm's above 300mm then definately go for the 70-300 DO it's just far more practical for everyday use, only get the 100-400 if you need that extra range. Remember that all of this is just my opinion and is based on just the one copy of each lens that I have owned, if you try them both for yourself you may decide differently so I would recommend you do this before making your decision.
Hope this helps!