These collections of words are based on the frequency lists published by the National Korean Language Institute, which can be googled up using the keyword “현대국어사용빈도조사결과파일”. 21st Century Seonbi provides a better introduction to this list than I could ever do.
What follows is a highly personal and idiosyncratic attempt at classifying these words in order to facilitate their learning. I've tried to discover and respect the patterns that appear naturally in Korean. The classification cuts across categories such as parts of speech, semantics, etymology and phonetics. Thus, you will find sections devoted to, say, native Korean words for mammals, verbs ending in -거리다 (which tend to describe certain types of repetitive actions), words that contain specific hanja (which classify themselves semantically, how nice), etc.
I'm not actively maintaining this section. The Nouns section is the one I've worked the most on by far. It's worth a look.
I'm indebted to J. David Eisenberg's extremely nice Introduction to Korean for my first hangul lessons.