I have the Dude installed on a Windows 2003 Server, with two other servers set up as agents, to help distribute the probing of devices.
Yesterday one of the agent servers went down, causing all the devices being probed by it to be listed as down and sending notifications for each service.
Is there a way to set up the agents to fail over so if one goes down the other picks up the slack and my inbox does not get bombarded by false positives?

You can't assign failover, but you can set dependencies of you devices to you agents.
Look at this post http://forum.mikrotik.com/viewtopic.php?f=8&t=36824

You need to create(if not already created) device, with same IP as agent, with (optional) one "Dude service" in it.

Thanks Sady. You're right, it's not a failover, so nothing probes those devices when their agent is down, but it is MUCH better to have them all just go grey until the agent is back online, rather than throwing a few hundred emails and then a few hundred more when the agent comes back online.

If you need more "Failover" look alike you can create double set of your devices.

One map with DevicesArrayA->AgentA, DevicesArrayB->AgentB
Second map with DevicesArrayA->AgentB, DevicesArrayB->AgentA

Every physical device will be represented by too objects in dude.
"->" means "access throe that"