Is there any great detectable difference in the ride? Is it worth upgrading from the older version? And does the boost valve shock on the higher models make any difference?

Yes, there is a big difference. I have got a Trek Fuel EX9.8, 2009 carbon bike that is much stiffer and has more active and "bottomless" rear suspension.

The 2010 EX models are even better because of Fox RP rear shocks with Dual Rate Control Valve and 15mm QR forks (EX8, 9, 9.8 and 9.9 models).

Trek's Full Floater suspension in combo with Fox DRCV dual chamber shock feels kind of Specialized Brain suspension, but without the Brain's "on-off" feeling. Fox 15 mm QR forks feel remarkabley stiffer, specially if you are a heavier rider and / or cornering on soft soil / sand.

Braking performance is much improved (the suspension actually works properly under braking on the newer versions)

I had a 2007 EX 9.5 which felt quite stiff, it suited me, but it was nowhere near as plush as a Stumpy or similar. Now got a 2010 Top Fuel 9.9 and it's a very different bike, incredibly plush, pedals really well too. I can only assume it's more noticeable on the longer travel models.

I have a 2007 Ex 9.0…couldn't stretch to a carbon one this time, so would be swapping over most of the bits onto an alloy version…

Not so bothered about the stiffness of a 15mm axle fork – I have a qr Magura Menja which I'm happy with and feels way stiffer anyway than qr Reba's and Fox's I've tried.

It was mostly the pedalling performance (and mainly uphill) I was interested in. Seems the 2007 version needs propedal on or a higher than recommended air pressure to pedal without bobbing.

I'm on an old style trek top fuel, and it does stiffen up under braking. I try not to brake on the bumpy bits if possible