I have grouped the literature per subject. I will try to keep this issue up-to-date.

Exception flow

• Static Analysis to Support the Evolution of Exception Structure in Object-Oriented Systems by Robillard, Murphy. This is the paper of which I am currently trying to implement the algorithm.
• Analysis and Testing Programs with Exception-Handling Constructs by Sinha, Harrold
• Interprocedural Exception Analysis for C++ by Prabhu et. al

Call graphs

• Scalable Propagation-Based Call Graph Construction Algorithms by Tip, Palsberg
• Call graph construction in object-oriented languages by Grove, DeFouw, Dean, Chambers.

Type Inference

• Type Analysis for JavaScript by Jensen, Møller, Thiemann
• On Using Static Analysis to Detect Type Errors in PHP Applications by Kneuss, Suter, Kuncak
• Object-sensitive type analysis of PHP by van der Hoek, Hage

PHP specific

• Variable features usage patterns in PHP by Hills
• An empirical study of PHP feature usage by Hills

Other

• Simple and Efficient Construction of Static Single Assignment Form, by Braun et. al. This method is used in the PHP-Cfg library, which in turn is used by the PHP-Types library, for constructing the control-flow graph.