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Some threads here from users with Flashed Cards talk about corruption issues though, scary...

What about the Hackintosh issue? Also since my Mac is 2nd hand, do I register it somewhere? (For insurance etc)

If you buy the wrong card, absolutely. I bought the right one, identical in looks and memory size (2gb) to the mac edition card in every way bar the apple label. Made sure the seller had a returns option so I could test it. After flashing it is in essence a mac edition card now inside and out.

Hackintosh is another issue altogether, all you are doing is putting a mac EFI bios onto an identical reference design card.
 
I upgraded to an MSI HD7870 (R7870-2GD5T/OC) in a MacPro3,1 after my GTX285 decided to immolate itself. Cost me about $125, and no flashing needed; just popped it into the system and it works in both 10.9 and Windows 8. All the ports function (both Mini-DP, DVI and HDMI) and I can drive 3 displays with no problems (2x MDP, 1xHDMI). The major downside to not flashing is you don't get any video before a OS loads; not a huge problem but it does make it a bit of a headache to troubleshoot booting issues or to select an alternate boot device (BootChamp makes this a bit easier). I've been back and forth on flashing to get full EFI boot support but, since I have a spare (albeit old) card to do debugging with, I haven't flashed the 7870 yet.
 
Hmmm... Now the question is which one would last me the longest, the HD 5870 or the GTX 685... Which is more durable/better built? What is the shoe horn or whatever you call it on the 5870 for anyway?
 
I am actually fine with the GT120, but would like to know if there quieter GPU's available for the 4,1?

My machine is noisy, not sure if it is the GPU but trying to figure it out by process of elimination.
 
The extension on the 5870 is the bracket that holds the card in place. It's how you can tell a card is actually designed for a Mac Pro. Fits great, and is a very positive fit. Not really necessary unless you tend to operate your Pro in a tumble dryer or Blue Angels F-18, but nice to have.

I have a 7950 in my 4,1, and it works great. It is fast, much less noisy than a 5870, and crushes it in performance. Except for Bioshock Infinite. Which is total rubbish. The GT120 would do better, but that is a coding problem. So I have to play that in Windows. Pretty much everything else screams. Since you say you are happy to play in Win, I'd grab a 7950 and go with it. I have a flashed MSI Twin Frozr III 7950 card in mine, and I've run enough torture tests on it to be confident the rest of the Pro will melt down around it before that card lets go.
 
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Hmmm... Now the question is which one would last me the longest, the HD 5870 or the GTX 685... Which is more durable/better built? What is the shoe horn or whatever you call it on the 5870 for anyway?

For the 5870HD, this card still works fine on my machine. I could not comment on the GTX685 as I haven't used that card. PC graphic cards are also popular among Mac Pro users for 2 reasons- better pricing and better performance. There are more choices being offered with PC cards compared to the Mac versions. If I am not mistaken, the OS ML 10.8.3 or newer have most of the Nvidia drivers.

A used 5870HD Mac version goes for around $280 to $320 Some good PC cards goes for $250
 
I need an video upgrade as well and have the OP's Mac Pro, only flashed to 5,1. Is a flashed 680 equivalent to the Mac edition in every way?

You can buy the same physical card from EVGA and flash it with their own BIOS. I can't see how it would be any different.
 
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