Best Practices for SP Administration:
1. Don’t create too many Web applications. Its specified that 4 web applications are enough on a server.
a. Intranet / Portal
b. My sites
c. Team sites
d. Partner Access
2. Don’t mess up with IIS settings of Central admin. SP likes to save the changes to Config DB, and Central admin works well as far as IIS Settings and Config settings match.
The only change which has to be done at IIS for Central Admin is SSL Settings.