Thanks for your comments guys, the high lamp settings are even better too.
Last night I made use of one of the more hidden settings: Adaptive Contrast. Now normally I'd stear well clear of this type of setting, but the disc we were watching (Perrier's Bounty) started with lots of darker scenes and seemed to suffer from raised blacks, making it look washed out. I tried setting the Adaptive contrast to +1 (out of 30) and it instantly stopped that washed out look, but without effecting the brighter scenes. It does slightly crush blacks on good discs and test patterns, so I wouldn't use it all the time by any means, but it worked well in this case. Not unlike the dark scenes in 'I am Legend' I suppose, with their raised blacks. It's a different effect to just moving the brightness down or even tweaking the gamma (I tried both after the film on a paused scene), so it's a useful tool to have, even if it's not 'as intented' it certainly looked better to me.
I've seen a few discs lately that seem to be authored in this way, so having a 'quick fix' button option is great.
I also played with the sharpness controls for use with my PVR memory setting: It added a bit of clarity to the picture, but without causing the micro judder that using my projector's equivalent controls seem to. I didn't check it with a test pattern, to see what it's doing to 'real data' but the settings were very low and with the M3D you can flick between copied memories instantly to compare the effect of one setting change and I prefered the result (at least with the PVR).