Her last Star Trek related cinematic work was in the 2009 reboot Star Trek. The lens flare-iffic clip below has her mocking young Chekov:
But her last Star Trek related work was the 2010 MMORPG Star Trek Online. I'm not certain how much she recorded for it, how much is clips, and how much is her impersonator, Lani Minella.
She also did some recording for Hamlet A.D.D., an animated film that wasn't released until 2014.
Of course, ever the forward thinkers, Majel had recorded herself phonetically, so that future technology can be used to ensure her voice can continue to be used. As the official Roddenberry twitter says:
Majel's voice is recorded phonetically,
& we're working to get her voice for things such as Siri,
maybe voice of the computer on #STDiscovery
1:55 PM - 4 Sep 2016
So, its possible that we will see her voice future episodes, through the magic of science fact.