Joan of Arc was finally declared innocent of heresy by Inquisitor-General Jean Brehal on 7th July 1456, 25 years after her death at the stake.
Some more modern cases of those found innocent or pardoned after their executions:
More than 300 British soldiers shot for cowardice or desertion in World War One 1914-18. The link is to a BBC article including personal stories. However, the Army Act of 2006 that enacted the pardon stated that it "does not affect any conviction or sentence."
Lena Barker, a black maid sent to the electric chair in 1945 for killing a white man she said had enslaved her: pardoned in 2005. The link is to the US National Public Radio site, including an audio podcast.
This year, relatives of Admiral John Byng, executed in 1757 for failing to "do his utmost", petitioned the Ministry of Defence for a posthumous pardon, but were turned down.