GNS3 is a graphical network simulator that allows you to design complex network topologies. You may run simulations or configure devices ranging from simple workstations to powerful Cisco routers. It is based on Dynamips, an IOS emulator which allows users to run IOS binary images from Cisco Systems and Pemu, a PIXOS emulator to emulate PIX firewalls.
WANsim allows you to simulate (more accurately, emulate) a WAN connection. In particular, it allows a user to change the emulated WAN speed, latency, variation, packet loss, packet duplication, and packet corruption aspects. It is configured as a network bridge that is established at boot time and uses the Linux Kernel NETEM functionality to accomplish its goals. Although relatively well documented, this functionality is not the easiest to use. WANsim wraps it into a simple to use script.
Cloonix is a Linux router and host simulation platform. It fully encapsulates application, host, and network l2 and l3 into a relatively easy-to-use simulation GUI. Network delay and loss characteristics can be configured per link. It provides support for running kvm or UML virtual machines configured into an arbitrary complex network configuration. It is possible to run a 12 router UML simulation on a small x86 host (a P4 with 512 MB RAM). 32- and 64-bit KVM machines are provided.