I'm remodeling my Bathroom and I had to lay down new 2 x 6" T&G boards. I plan to lay tile so I bought Hardiebacker (cement backer board). I was planning on laying down the backer board, lay thinset over T & G boards then backer board, but after reading a lot of sites I'm not sure if this is the best way to go. My tile area will be about a 4' x 5' foot section on the floor. I'm also reluctant to put down 1/2" plywood then backer board then tile because it will create a big lip between the bathroom and hall way.
Cement board is brittle and is not suitable for unsupported use as a floor. When it is supported by plywood or such it is much more resilient provided they are sufficiently bonded (screws work fine as iLikeDirt mentioned, but some like to supplement that with construction adhesive for a quieter floor. On the other hand, there are alternatives to cement board. One system is thinset over lath which you can easily do at 3/16" or if you are careful at 1/8". However this is a much more expensive system, more brittle (add underfloor bracing) and more difficult to do. It also needs lots of staples.