It means "I am happy to have done X". As a reply to "It's my pleasure to have you on my friends list", it means that you are also happy to have that person on your list.
While it can be used after meeting with someone, it can also be used after giving help and the person thanks you. It's similar to "You're welcome". For example:
- Thank you so much for helping me with organizing the meeting today!
- The pleasure is/was all mine.