Determining what is good vs what is bad traffic I think is more of an art, and also depends on your business needs. From what I've found, you really need to understand how to profile the different traffic as far what is and is not tolerant to dropped packets.
If you are using VoIP, no matter what that should be a priority. Where I work, Telnet and Citrix are key methods to our business critical systems, so I have those set rather high too. Internal HTTP traffic is favored over Internet HTTP. I could post how I'm marking traffic, but I don't think it would be much help without understanding better what every application is for.
Another thing I should have mentioned, on my edge (which is my connections back to the corporate head quarters) I'm running CBWFQ. For my metronet connections I'm using CBWFQ and Shaping where possible.
The thing I don't care for in the Cisco guides for QoS is how they label the queues. I try very hard when I'm talking to my customers to not tell them "well, your traffic is in the Bulk queue, not Mission Critical". I know I'll have directors jump me because everyone thinks there applications are the most important.