My favorite Glee cover would have to be a tie between "I Dreamed a Dream" by Lea Michelle and Idina Menzel and "As If We Never Said Goodbye" by Chris Colfer.
The tension and camaraderie between Lea and Idina's characters is so palpable and I think everyone was excited to see Wicked's Idina play Rachel's mother; she was a perfect actor to cast in the part.
When Kurt is wandering the halls of McKinley High and singing "As If We Never Said Goodbye", you feel the emotions he's feeling and you empathize with his struggles. Not to mention, the vocals are amazing - such an impressive range for a man.
Oh, and I also love Songbird by Naya Rivers... because I love Fleetwood Mac :)