How can I analyze and annotate multiple (500) games with stockfish? I want to analyze multiple games in one batch with Stockfish. Apart from Scid I do not know any other tool which will do it faster or better. What are som alternatives to Scid with better performance or annotation quality in mind?

Scid allows me to set time or depth (not both at together), put score, put variation, multiple lines analysis.
If you are using Android, Analyze This (Free) is the way to go, just use the 'Auto Analysis' feature.
If you are using windows, Arena Chess is the way to go (you need to install Stockfish, and load the games in a single PGN, and turn on Auto Analysis ...)

Hope this helped, ~CSS