The Khmer Empire reached its zenith under king Jayavarman VII in the thirteenth century. During this period the Empire stretched across most of mainland South East Asia - he embarked on an extensive building program and famous temples such as the Bayon were built in his new capital called Angkor Thom.
From the end of his reign the Khmer Empire started a period of decline with no end. Historians put forth a few different reasons for this:
The switch from Hinduism as the state religion to Theravada Buddhism. It is thought that the loss of respect for the 'devaraja cult', (the idea that the king was a universal monarch associated with a Hindu god like Shiva or Vishnu) resulted in a loss of enthusiasm for a centralised state power system. This may be why we see a lack of building projects during this era.
On that note of building projects... The city of Angkor ran on a very technically astute and complex set of canals and reservoirs which held massive amounts of water in what is referred to as 'an hydraulic city'. This infrastructure required a lot of maintenance and if this was impacted by the change in religion it would have had a terrible impact on the viability of the city.
Environmental factors: Archaeologists and scientists have recently suggested that extended periods of drought or flooding would have seriously impacted the aforementioned hydraulic infrastructure of Angkor. This could have led to the stagnation of these waterways which may have led to outbreaks of malaria. Basically without the rice surplus that was created at Angkor (which was the largest pre-industrial city I might add) then the Empire could not support itself. Imagine what it would be like if all the roads and trainlines in any major modern city ceased to function -- things would soon get bad enough to just abandon the city.
The rise of the kingdom that would become Thailand in the West was also a large determinant in the decline of Angkor - the Thai sacked Angkor in 1431 - and the capital was moved closer to its current location in Phnom Penh after that.
Historian David Chandler suggests that the Khmer Empire never disappeared, but rather undertook a centuries long transformation into the Cambodia we are more familiar with today.
I would recommend his history of Cambodia or the documentary series 'Jungle Atlantis' (http://www.dailymotion.com/video/x27k4gn) for a better break down of some of these concepts.
Also I have started a podcast on Cambodian history called 'In the Shadows of Utopia' which can be found on itunes or Acast (or at http://www.shadowsofutopia.com/episodes.html) if you are interested in the decline of Angkor and how it figures in the grander scheme of Cambodian history.