The Top Five
1. MRTG - The Multi Router Traffic Grapher (MRTG) is primarily designed to monitor and graph traffic on network links. It is written in Perl, generates HTML with PNG image graphs, updated at configurable intervals. One of the best features is that it creates daily, weekly, and monthly graphs as well. You can monitor any SNMP variable you choose. In my opinion, MRTG is one of the best tools ever written for network monitoring.
2. Cacti / RRDTool - Cacti is a front end to RRDTool, and uses a MySQL database for data storage. Data sources can be created and customized. The front end is written in PHP. Many templates are available, as well as the option to grant users permissions to view only or create new graphs.
3. Nagios - Nagios goes beyond network monitoring to include notification and problem management, as well as other enterprise-class features. It has been around for over 10 years, has a large user base and support community. While some of the solutions in the top five are OS agnostic, Nagios runs on Linux or Unix. You can monitor any system or device with it, of course.
4. Ntop - Ntop is focused specifically on network traffic monitoring. IP traffic and protocol information & statistics. Information can be sorted or detailed by host, subnet, or viewed in total for the network. Ntop works with NetFlow and sFlow as well. Interestingly, it can be compiled for Windows as well as Unix.
5. Zenoss Core - If you're looking for an enterprise management platform for more than just the network, but don't have the budget for a commercial product, Zenoss has an open source alternative. Zenoss offers Professional and Enterprise versions with support and consulting available.
SolarWinds Cisco Netflow v5 - This and several other SolarWinds free tools are excellent. If you have a Cisco network with Netflow this can get you started.
Snort - Snort is technically an IDS (and one of the best), but can serve as a great application layer network analysis tool. I didn't include this or any other IDS as they are really a separate category.