There are lots of synonyms in WK that make it difficult if you start learning in the other direction (English → Japanese).
This situation is made even worse because we as learners do not yet have the same feel for the language as native speakers do. So we can’t always make a good judgement whether two things are synonymous or not.
For example, English learners may not be 100% sure whether to buy and to purchase are synonyms or not. They are used in different contexts, but are practically synonyms.
An example in Japanese is 皆さん and 皆様. They both mean “everyone”, but in WK one is “everyone, everybody, all”, whereas the other is “everyone, all, everybody”.
This results in difficulties when using, e.g., KaniWani or @rfindley 's Self-Study userscript .
I’m basically creating this thread for myself, to collect all words that I deem to be synonyms, but you can of course reply with your own contributions and then we can discuss here whether the words you mention are really synonyms or not.
EDIT: the second post of this thread is now a wiki. Try not to post a question in the wiki, but ask your question in a new reply because otherwise other people may not see your question (especially if the wiki becomes long-ish).
If you’re a regular/leader, you can also post your own reply and turn that into a wiki.