The title says it all. I reached my daily limit today and noticed that one of my questions was upvoted after I reached the daily limit.
What happens to the reputation? Do I get it tomorrow or is it lost into the ether?
Receiving upvotes after hitting the rep cap have do not alter your reputation, neither at the moment nor at a later date.
You can earn a maximum of +200 reputation from upvotes and suggested edits in any given day. Bounties and the bonuses for accepted answers are counted separately (source). Reputation “lost” from the reputation cap is not awarded on following days.
Just to add a bit to the main answer: upvotes you receive beyond the rep cap are not entirely useless, as they'll cancel out subsequent unupvotes on an upvote you receive that day. (That is, when you get unupvoted, it's as though the original upvote never happened; but if you had "extra" upvotes that day, some of them can cover.)