It really depends on your budget and how much time you have.
Flights will get you there nice an quick, but are comparatively expensive. I think Bangkok Air has the only direct flight hence they keep the prices high. You would have to fly via KL on Air Asia.
Buses will take a fair bit of time (10-12 hours I think??), and I understand there can be lots of hassle if you don't pick your bus company carefully. People have reported of various problems and so-called 'scams' at the border. Having said that, people have also experienced hassle-free bus trips there as well. The road used to be pretty rough on the Cambodia side but it has improved over the last couple of years.
Search through the forums and you will find a fair bit of discussion on this that will help you decide.
If doing it by one of the Khao San Road buses it will probably take forever.
But if you get the public bus to Aranyaprathet and then share a taxi with some other travellers once over the border (think its about $45-50 for a taxi) it shouldnt take more than about 7 hours for the whole trip