Barring this, are there particularly well-regarded reference sources for this?
Pending more technologically advanced solutions (such as those mentioned in the answers posted here), I've started a manual glossary. Please contribute to it!
We should have a glossary. Every user should be able to send words they don't know to the glossary, and the knowledgeable users can write a definition.
This way only words that are actually used on the site will appear in the glossary.
There would also be a way to link words, so that (for example) different transliterations of the same word would be linked.
I'm imagining something like the NYT quote bubbles Dori describes in her post, but instead of connecting them to tags, they would be connnected to Glossary entries. Each entry would have the entry and definition. This could be used for words and concepts. In addition, I'm really excited about using such a system to give glossary style definitions to people and books quoted, so that we could easily have context when quoting someone. (e.g. if an opinion is quoted from the Rashba and another opinion from the Mishnah Berura, the glossary information could tell us when and where the authors lived, and when the sefer was published.)
As discussed in the past (see further down along that page also, e.g. to this and this), there is interest having some sort of automatic glossary on the site. Perhaps Dori or someone else who works for SE can weigh in with the prospects on that (including a possible ETA), so we can know whether it's worthwhile starting a 'manual' one meanwhile.
In my opinion…
I think that the right place for this type of information is the tag wiki.
For example, if you want to know what muktzeh means, just hover over the muktzeh tag on main:
The NY Times web site has a feature where, when you select a word or phrase, a little ? bubble appears:
If you click on the bubble, you get a definition of your selection.
I'd love to see similar functionality on Stack Exchange. That is, you'd highlight some text, and if there's a tag with the name of the selected text, and that tag has a wiki entry, a similar popup would appear showing the definition from the tag wiki.
Short or long term, though, there's a problem:
Unfortunately, this site's tag wiki isn't suitable for either approach, due to the odd way tags are used here. I understand the historical reasons for your tags (the site began as a SE1.0 site which didn't have synonyms); what I don't understand is why they're still like that.
[Okay, okay, I understand the most likely reason… ]