Following are the tools for monitoring a linux system
System commands like top, free -m, vmstat, iostat, iotop, sar, netstat etc. Nothing comes near these linux utility when you are debugging a problem. These command give you a clear picture that is going inside your server
SeaLion: Agent executes all the commands mentioned in #1 (also user defined) and outputs of these commands can be accessed in a beautiful web interface. This tool comes handy when you are debugging across hundreds of servers as installation is clear simple. And its FREE
Nagios: It is the mother of all monitoring/alerting tools. It is very much customization but very much difficult to setup for beginners. There are sets of tools called nagios plugins that covers pretty much all important Linux metrics
Munin
Server density: A cloudbased paid service that collects important Linux metrics and gives users ability to write own plugins.
New Relic: Another well know hosted monitoring service.
Zabbix
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