I had the privilege of reviewing a neat paper, Network Topology Discovery, by Eric Siegel, a technical analyst at the Burton Group. His paper covers a many aspects of network topology discovery in 30 pages, sprinkled with details on how things work. I found it to be a very well written paper, covering the topic very thoroughly. I can't promise that the paper is free (their business depends on selling their papers). If you're interested in a copy, contact Eric at esiegel@burtongroup.com. He will put you in touch with the appropriate sales person at Burton and it's up to you from there to convince them that you deserve a free copy. ;-) Subscribers to the Burton Group's services will be able to download it for free.
Topology discovery is an interesting topic and is one that we have worked hard to implement well. We recently had a customer decide to use our products as the 'master repository' of device discovery, due to the accuracy and depth of the resulting inventory. A key component of discovery is classification of the discovered devices. Knowing that a device is a router, a switch, or a Linux system performing routing and switching, or a Cisco ISR that performs routing, switching, firewall, and wireless are important data to knowing what's in your network and being able to track down problems caused by those devices.
-Terry