heh.
Alot of tricks to that.
First and foremost get as much polish as you can into your 3D renders. Make sure there is enough contrast in them to provide depth, and also do not go pure black or white in shadows or hilights.
Also render alot of your pieces in seperate passes so when compositing you can adjust them individually.
In AE, alot of the lighting drama acheived is done by the use of many masked layers of the same 3D with soft edged masks, each layer destined to be hotter or cooler than the one further back (still speaking of one element, not the whole scene).
Knoll Light factory used NOT for flares bu for creating overlayed ‘hot spots’ is very invaluable as well. Ofcourse flares are a part of it as well, but custom flares,…never the standard cheese flare.
Shadow layers that force depth on the environmental 3D pieces helps as well, these are simply black layers with animated soft edged masks.
And finally, judicious use of depth of field either real or ‘faked’ to give a sense of depth.
Final note: There is ALOT more to it than just sweeting the 3D,…..the whole concept of the piece and ‘environmental space’ that the 3D esists in is what makes these works so nice. A bad layout with a simple 3D type fly in would not look near as nice with all these tricks as would a well thought out ‘environment’..
The environment is what gives the 3D the epic sense of size and the ‘hero’ logo that is so sought after.
Good luck!