Money Moral Dilemma: How much should I pay my ex for her share of our flat?

When I was in the same situation, I gave the ex his share based on the current value, minus the outstanding mortgage etc. I told him what I thought was fair and he snapped my hand off, thinking he’d have got less.

Whatever you decide remember this is somebody you loved or presumably you wouldn't have bought a place together. Good endings are important to moving on properly. No matter what happened between you, letting go and forgiveness are important for YOUR future happiness. You can afford the whole place by yourself; what is her situation, are you struggling? These questions are what makes this a MORAL dilemma.

I doubt very much that the value has gone up all that much in the past twelve months, there are regional variations in house prices, the national market seems to be slowing according to Halifax and Nationwide, so unless there are reasons why your area is special in someway (such as new road or rail infrastructure) I would say that it is pretty academic as to todays market price or last years.
Having said all that on principle it should be the current market value minus an allowance for the mortgage payments she missed as others have said.
There is an online house price valuation service - I cannot remember the name of the site - which allows you to put in your postcode and the yearly quarter (i.e. 2009 Q1, Q2 etc) you purchased your property which gives a rough valuation now based on no substantial property alterations. I would use this myself.