I work at borrowlenses and after having access to both, I actually made the switch from my D7000 to a 5d3; sold all my lenses and now picking up some canon glass. The d800 is impressive and of course, its has all the high IQ bells and whistles but in the end, I figured that:
-90% of my photos are going to be on the web or view on a computer, down scaled and uploaded to facebook or make 4x6 prints at costco by my clients. I doubt they will be printed in huge canvases, so pixel count does not matter to me.
-D800 needs both hands to change the WB and ISO. The buttons are so awkwardly placed that you'll need to take your eye off the viewfinder to look for it. The 5d3 only requires one hand while I keep my eye on the viewfinder info display. Its quicker, faster and less fumbling around.
-Green/yellow cast on the D800's LCD display. No thanks, I want to have an accurate representation of my exposures.
-Double filesizes for the d800. 14 more megapixels and all of the sudden each raw file is 45-50MB? My i7 OC'ed to 4GHz and on 14GB of DDR3 workstation seems to bog down on Lightroom 4 when loading D800 raws. Sorry, I dont want to wait while im batch editing wedding or event photos. If you're the kind of person that only takes 5-6 carefully dialed in shots on a tripod while manually white balanced to perfection, then yeah, I see why the d800 is in favor. When im on a job running and gunning while my subjects are in dynamic lighting environments, I dont have time to waste on LR4 loading 2,400 RAW files just to fix tiny but annoying exposure/WB screw ups later on. Not to mention constantly swapping out expensive high capacity 500x + UDMA CF cards
-Fully customizable controls. The D800 gives you what, one fn button? The entire shutter button side of my 5d3 controls has been completely remapped to my specs.
-Nikon lenses are fragile. I swear, they'll break if you look at them wrong. The 14-24, 24-70, 80-400 have zoom mechanism become stiff and/or completely fail after a few years of constant use. I've never seen a canon equivalent exhibit such hilariously awful life expectancy. They are absolutely fantastic lenses, worth every penny of their premium, don't get me wrong. But then the fotodiox F to EOS adapter with an aperture adjustment lever exist. You can mount F lenses on a canon, but its physically impossible to go the other way around because of nikon's smaller mount diameter.
-Built-in pocket wizards on new canon speedlights. Doubt Nikon will implement that anytime soon since they just released the sb-910 and 700
edit: added more lingering thoughts / fixed grammar