Nick,
This has been discussed many times on Pistonheads and on Rennlist - Rennlist really is the best place to research these cars. As Andy says, you primarily pay a premium for the exclusivity of the 3.6 but also the extra power and looks (mainly the Speedlines). 3.6's are increasingly seen as collector's cars and as such will only rise in value - you will be lucky to find a reasonable one for less than £40k, and for a good one nearer £50k now. Reasonable 3.3's start at around £20-22k and rise up to c.£30k for areally good one. The 3.3 won't lose any value if properly maintained, the 3.6 will only increase in value.
Both are esaily tuned - remove the cats, replace the headers and up the boost (not beyond 1bar) and you incresae both the power and the torque - c.360bhp on a 3.3. Add a larger turbocharger and that will give you even more power (c.380bhp+ on a 3.3) although the peak will be higher up the rev range. That lot will cost you around £4k. So, for c.£28k (less if you buy one with those mods) you will get a 3.3 that out-performs a standard 3.6. Add a set of replica Speedlines for £1.5k including tyres and for £5k you have a car that is only the true enthusiast would be able to tell wasn't a 3.6.
However, these cars are much more expensive to maintain than a SC or 3.2 - think £3k a year minimum on servicing and maintenance, and the upgrading/modifying bug is very easy to catch! I have owned my Zermat Silver car for 3.5 years (see the picture below) and I have spent c.£18k including a top-end rebuild due to a broken head stud (95% maintenance; my upgrades replaced worn-out OE items); the blue car next to it has had £30k spent on it in the last 5 years (£20k maintenance - including £10k on a top-end; and £10k on upgrades) and I know another owner who spent £40k+ on his over 3.5 years (probably 50% maintenance, no top-end; 50% upgrades). Head studs breaking are a very common, seemingly age rather than mileage-related, problem and asa result many people look for cars with a top-end rebuild, especially if they are planning on increasing the power - therefore you need to buy on condition not mileage.
That red car that Josh has just bought was a prime example of the right car with the right mods at a good price. I guarantee it won't be cheap to maintain, but it will more than offset this with the lack of depreciation and the enjoyment he'll get from it each and every drive! Personally, I have also made some very good friends as a result of owning my car - so it has been more than worth it!
Cheers,
Tim.