In general I would say there is no such universal resource.
There are websites that can give you nice deals but they are far from complete, they will not give you a route (A->B->C->A). For instance, Ryanair usually does not show up in such planners.
My advise is:
Start by finding a cheap flight somewhere interesting to you. Than you have to start looking from there. You have to check where you can easily go from that place and if it's worth going. You also have to match that with your interests. I don't see a particular purpose in going somewhere cheap if it has no particular interest to you.
Look at low cost airlines, train connections and bus to find the best deal for each situation.
To search which cities are connected by low cost plane companies look in flycheapo.com. You can also look directly at ryanair website or easyjet for good deals but flycheapo will give you many more ideas of low cost air-lines.
For train you have to look yourself in each country. You can also use the german train website. It has some european connections. Central europe is very well connected by train and in many cases it's better than flying (you get out in the city center saving time and avoiding airport transfer costs). Look at the link in "Local public transport route planners" for more train companies websites.
For bus I would recomend looking at eurolines. They have very nice deals sometimes.
Local public transport route planners
For travelling inside a country you can also check local route planners. These won't exactly give you the cheapest price but wil help you get around in a country. Look at this question
Remember that, in general, if you book in advance you can get better prices.