Minecraft is not a serious solution. I could get it to work but it would be terribly uncomfortable to read and edit, almost certainly worse than layered 2D spreadsheets.

Currently i'm making a constructed language and trying to work out what all the possible syllables are given the fairly simple syllable structure. There are tools specifically for this, but there have been other times when a 3D spreadsheet would have been very helpful even if i can't still remember what problem i had.

Another example, also for constructed languages, is tables of conjugations and declensions in fusional languages. That is, a language where a single prefix or suffix indicates a specific case, person, number, etc. and there are a bunch of these that need to be mapped out.