What's is Main (by Tobias Nipkow) contains a list of populer datatypes and functions (i.e. there signatures) in the Main theory.
A Proof Assistant for Higher-Order Logic (by Nipkow et al.) is an extensive tutorial to most of Isabelle's features. Find explanations for most methods, tactics, … via the index.
For a list of pre-defined symbols in Isabelle/HOL see Appendix B of this document. Useful when the set of UNICODE characters is not available.
"Executing Higher Order Logics" is a paper making an overview of how to write functions on Isabelle/HOL and some performance issues. Good about it is that it has some code and goes over some concepts that we've seen in the lectures/tutorials