I recently rewatched all three, and they all hold up as I remember. The first one is great, the second could be great if there was a bit more editing to trim down some overly long monologues, and the third one is a bit meh.

In The Matrix 2, Trinity uses nmap to check for an ssh exploit, then cracks it using a cli tool, all from Linux.

Edit: The ssh exploit was a real, known vulnerability at the time.