I recently visisted Prague and fell in love with the city…
In the future I would like to buy a second holiday home there…
I read up on the government webpage about getting a residence visa and it seems that you can only move there basically if you marry a Czech citizen. Once they join the EU will citizens of other EU nations be free to purchase property and live there?
Yes, this is one of the most basic effects of the EU. Every citizen of one member state may vistit, move (permanently) to, work in and do business in every other member state like a native citizen of that state.
I think for the new members the full rules may not apply , at least for a few years. Instead there will be interim arrangements to protect the citizens of the new member states. For instance there were big worries in Poland about individuals and companies from western Europe going in and buying up all the farmland at a very cheap price. So now there will be rules for the first few years limiting the percentage of farmland that can be bought by non Poles.