Scarroll has posted up some FAQs to answer some common questions that we are asked about the profiler.
Profiling FAQ #1: Why doesn't my Sampling Call Tree look like my Instrumentation Call Tree
Profiling FAQ #2: Why am I seeing functions from DLLs I didn't instrument in my Function view?
Profiling FAQ #3: How do -exclude and -include on vsinstr differ from -start / -suspend / -resume, etc.
Profiling FAQ #4: The top sampled function is [ntdll.dll], now what do I do?!
Also, check out his blog for some analysis on several interesting papers from the research world.