11 Ways to Combat Botnets:
1) Install a Windows Firewall: Also, properly configure it.
2) Disable AutoRun: Do not let systems automatically install software.
3) Break Password Trusts: Take control of admin accounts and don't let systems automatically connect to each other.
4) Consider Network Compartmentalization: Set up VLANS, or access control lists (ACLS) between subnetworks and limit the capability for computers to communicate with each other.
5) Provide Least Privilege: Give users what they need to do their jobs and nothing more.
6) Install Host-Based Intrusion Prevention: Don't let Botnets get root access.
7) Enhance Monitoring: The more you know the better so log it, log it, LOG IT!
8) Filter Data Leaving the Network: Botnets like to communication with the command and control center so egress filtering is key.
9) Use a Proxy Server: Forcing outbound traffic through a proxy gives you a point of monitoring.
10) Install Reputation-based Filtering: Block emails from, request to. Know your potential malware websites and filter.
11) Monitor DNS Queries: If a computer is responding to a DNS query could be a sign of a botnet infection.