Start-ups and organizations with limited budgets that are security conscious are often encouraged to deploy intrusion detection stacks. Given that prevention will always fail, intrusion detection stacks are often vital to learn why defenses failed.
I am a fan of the following intrusion stack covering the app layer, system layer, and network layer:
system: OSSEC
application: ModSecurity
network: FlowMatrix (i cheated, this one is not FOSS, but it's free!)
What are your favorite intrusion (FOSS or free) stacks?