Any A6 (or A4 probably) 01E 6-speed 4WD gearbox 2000 or younger would do.
I prefer the A6 Tdi boxes because they have a nice 0.56 ratio 6th gear. There is no sense running at close to 3000rpm at 70mph with that much power. The Tdi 6th takes it down to close to 2000rpm. My S8's mpg went from around 25mpg to around 31 for a motorway run just from the 6th gear swap.
There are some sites with lots of info about 01E, I will find and post links. If I remember correctly any 01E 4wd from year 2000 onwards has a wide 1st gear and 'flex' main shaft which enables it to handle a lot of torque. All the B5 S4's running huge torque over 500lbft don't have problems with their 01Es handling that torque, its a very tough gearbox.
I think (from the pictures) RS6's 4.2 engine is a 10-bolt to flex plate. You would either need a custom flywheel or perhaps the pre-face S8 or S4 flywheel might fit, I believe those are 10-bolt too.
You would need a performance clutch I'm guessing, I don't think the stock S8 or S4 clutch from the dealer will handle the amount of torque the RS6 can deliver. There are loads of performance clutches out there to chose from, AWE, JHM, etc. That may take a little researching to see which ones fit and which ones are good.
Here is one RS6 conversion:
http://www.rs6.com/showthread.php/22...d-RS6-with-01E
And it looks like MRC have done a RS6 conversion to manual too. I heard Unit 20 did one also.
http://audisrs.com/viewtopic.php?t=47211&start=0