The way I see it:
There are two advantages of having larger sensor size:
1) A larger sensor collects more photons, that's good for noise and DR.
2) A larger sensor would potentially resolve fine detail better using the same quality lens
3) Shadow noise depends much on sensor technology while factors 1-2 do not.
Regarding DoF it may matter little. With a larger sensor you may need to stop down more but a larger sensor will have better ISO and also better edge contrast on small detail (MTF), so you may stop down a bit more and still achieve the same quality. The 4/3 systems seem to have some very good lenses, but that advantage goes away if you stop down excessively.
In summary, I'd say that general image quality will be better with an APS-C sensor, especially as the Sony sensors seem to best of breed. Regarding DoF you will probably something like stopping down one stop more on APS-C.
Regarding cropping, what is relevant is how you crop. I usually crop according to image content and not to paper format.
You could also consider waiting a couple of months? Some interesting things may show up at Photokina. With digital we are not really bound by old film formats. Some new interesting concept with larger or smaller sensors may show up.
4/3 vs APS-C sensor size
We all know and accept that the two most determining factors to image quality are the sensor size (not necessarily the most # of pixels) and the lenses.
I am buying a small compact for when I don't want to take my 5DmkII out for 'street shooting' and want to have maximum image quality so that I dont feel compromised or that I cant make a large print (e.g. 16x20")
I am considering the Nex 7 or the Olympus OM-D.
Both are exccellent but on all counts except sensor size (and that the accessory grip is necessary for my big hands on the Olympus) the Olympus wins out for me - weather sealed, IS in the body, range of lenses, quieter shutter ...
the Nex 7 sensor size is 23.5 x 15.6mm
and the Olympus is 17.3x13mm
All along I've been thinking it has to be the Nex 7 for the larger sensor size, and it just occurred to me that aside from the proportional/ratio difference - one being 3:2 (1:1.5) and the other 4:3 (1:1.3) - they're not all that different (2.6mm in height) -the Olympus 4/3 sensor is really almost the same as using the larger Sony APS-C sensor but cropping the long dimension into the 4:3 format.