The most valuable component for better integrating models with basically anything else is a standard language for communicating the structure of those models. That language is XMILE. The draft specifications for this have been finalized and the standard should be approved in the next few months.
A Python library for analyzing system dynamics models called the Exploratory Modeling and Analysis (EMA) Workbench developed by Erik Pruyt and Jan Kwakkel at TU Delft. This package implements a variety of analysis methods that are unique to dynamic models, and could work very tightly with PySD.
An web-based app called Simlin created by Bobby Powers exists as a standalone SD engine. Allows building models and exporting them to XMILE output.
The Behavior Analysis and Testing Software (BATS) developed by Gönenç Yücel includes a really neat method for categorizing behavior modes and exploring parameter space to determine the boundaries between them.
The SDQC library developed by Eneko Martin Martinez may be used to check the quality of the data imported by Vensim models from spreadsheet files.
The excels2vensim library, also developed by Eneko Martin Martinez, aims to simplify the incorporation of equations from external data into Vensim.