I have a laptop and a desktop, both running LFS S2. The laptop is a Dell XPS gen 2 with Centrino 2.1ghz 1gb ram and 6800 ultra GPU. The desktop is a E6300 processor 2gb ram and a 7950gt GPU.

I compared the two FPS wise thinking that my desktop would come tops, but it matches the laptop, the laptop has a great screen and I can run 1900x1200 with 8x AA and 16x Anis and still get 70-90fps with 20 runners online, the desktop matches this but only at 1024 x 768 because I have a naff monitor ? but even so surely the desktop should hammer the laptop ?

Is this because LFS is not dependant on latest technology such as a DC processor etc . . ?

I'm not 100% sure, but it's sounds about right to me. The Ultra version is generally a lot more powerful than the GT version of any given card. Granted, the 6800 is one generation older than the 7950GT, but I think I would still put the 6800 on top when it comes to theoretical performance. (Especially since shader performance is largely irrelevant since LFS uses DX8.)

Furthermore, at your desktop resolution you're very likely to be CPU limited anyway (meaning your graphics card is idling a lot of the time), so you could probably push the resolution and AA/AF on the desktop a lot higher without losing any FPS worth mentioning.

EDIT: Also, make sure you haven't enabled vertical sync (either in the drivers, or in LFS) and that is limiting your framerate. For when you're "benchmarking" I mean...

EDIT2: As for your last question (damn, lot of editing ), LFS is very much dependent on a good CPU. A dual-core doesn't matter though as it can't take advantage of the second core. For LFS one fast core is better than two (or four) slower ones. This could mean that your laptop's 2.1GHz Core/Core 2(?) is actually faster in LFS than your desktop's 1.86GHz Core 2 Duo. I think that's the thing here. The processors are more or less maxing out so the actual graphics cards are not that relevant for performance (at low resolutions).

Quote from crosserboy :

I have a laptop and a desktop, both running LFS S2. The laptop is a Dell XPS gen 2 with Centrino 2.1ghz 1gb ram and 6800 ultra GPU. The desktop is a E6300 processor 2gb ram and a 7950gt GPU.

I compared the two FPS wise thinking that my desktop would come tops, but it matches the laptop, the laptop has a great screen and I can run 1900x1200 with 8x AA and 16x Anis and still get 70-90fps with 20 runners online, the desktop matches this but only at 1024 x 768 because I have a naff monitor ? but even so surely the desktop should hammer the laptop ?

Is this because LFS is not dependant on latest technology such as a DC processor etc . . ?

LFS only makes use of a single core. As LFS is very CPU heavy it means your desktop only runs as fast as possible on the single core.

7950GT GPU is a waaay faster than 6800Ultra, but LFS isn't able to fully utilize FX5200 when to comes to GPU-only power. Your desktop C2D is of course also faster than NB Centrino, but as Woz said, LFS is not able to use the real advantabe of second core. That's why Centrino doesn't loose that much.
I think that your desktop should be faster about 20-30%, but this difference would really show up when on 28-grided (viva la W9 patch). Then your NB would IMO produce much worse framerate than desktop.
Resolution will affect your performance by VERY low. Me having 7900GT TOP can play in 1600x1200 with 16xAF 8xS AA and my FPS dropes down by 2-3 in comparsion with 1024x768 no AA/AF.