Word counter using a word list and some text files
You should try to switch inner and outer loop, because it will be much faster to read each wikipedia articles in and count the word frequencies for all 500k words (you anyway have the 500k word list in memory all the time). What you do now is reading 500k times all articles into memory which is time consuming.

To sum up all usages of a word, you can use the map which already exists. Just read out the current sum for a given word, add the occurrences in the current article and write it back to the map. Right now you are just writing one entry to the map, convert it to a string and clear it right afterwards. I assume, you had the idea in mind to do it how I described.

Don't worry about Java execution speed in general, because the code will get compiled (just-in-time-compilation) to machine code eventually.