There is the The Nuance Thread 
, where users have compiled a list of similar words and their nuances.
Personally I don’t pay too much attention to specific meanings. I use WK for passive knowledge. I want to learn to read many kanji and words. In reading, I will never have to produce the word myself, and the context will pretty much always be provided. I use my Japanese teacher, grammar book, and Japanese friends for more nuanced vocab knowledge. Also, JP-JP dictionaries.