Both Rail Europe and Eurail suck IMO.
Prague to Krakow bought in Prague should be around 37 EUR (1000 CZK). It can be a bit more if you use a fast EC train or a sleeper (10-40 EUR), but this is a good estimate. I found the price using http://www.jizdenka.cz/ . The cheapest connections (for 37 EUR) are via Bohumín. Trains that go via Katowice should be around 40 EUR (1070 CZK), other connections will be even more expensive. (The longer the journey in kilometers the higher the price.)
You can find an online schedule for the trains at
http://jizdnirady.idnes.cz/vlakyautobusy/spojeni and
http://www.reiseauskunft.bahn.de/bin/query.exe/d
Both sites have English language option.
I prefer the German site www.bahn.de for online schedules as they have the best search engine for international travel in Europe. The czech site is good if you want trains in Eastern Europe and the exact distance in kilometers the train travels.