I can definitely recommend Justin Burls in Essex if you want a custom Ti frame, and it'll probably be cheaper than a lot of the custom steel frames already mentioned - currently £980 according to his site.
I got mine almost three years ago, and all I wanted was a Ti version of my KHS but with disc brakes and the headtube adjusted for short travel suspension forks. I sent him the dimensions, he sent back a drawing of the frame and with a bit of back and forth we decided on some minor modifications. He was happy for me to visit him (works from home in Harwich) to have a look at some frames and discuss the details, then it was just a case of waiting.
The frames are actually made in Russia, and I can't fault the quality of the welding on mine. He used to mainly do road bikes but is doing more MTBs and plenty of 29ers. He also makes steel frames himself, but they aren't much cheaper than the titanium.