At the end of Stargate Atlantis, after Atlantis lands on Earth, the fate of Todd the Wraith is left open. Last seen, he's a prisoner of Atlantis. What becomes of him?
In the series finale, "Enemy at the Gate", Todd seeks the help of Atlantis to destroy a ZPM-powered Hive Ship stolen by one of his underlings (the ZPM having come from the ones he stole from the Asuran homeworld). He provides Atlantis with two additional ZPMs after the initial attack fails, and remains in their custody (in Atlantis on Earth) once the Hive is destroyed. His long term fate is not elaborated upon; however, he was slated to play a part in the upcoming Stargate Atlantis film, however, the project was shelved indefinitely.
There was a book series called Stargate Atlantis: Legacy which takes place after series 5.
In the books Todd was put into stasis, and Atlantis returned to Pegasus. There they discovered the Wraith were uniting under a powerful new queen. Todd was revived and gave the team some information in order to fight the new threat.
For his assistance he was eventually set free, or something like that (its been a while since I went through the book series).