Popular stencils
Petri Nets
Petri Nets for modelling synchronization and non-deterministic processes (e.g. operating systems, workflows)
Cross functional diagram
I've used the cross functional diagram and this stencil several time to analyze the organization of different sized enterprises (SMEs and Big enterprises) for my consultancy work. It works well to define the organizational flow and to understand critical points within the organization.
Akka Streams
The Akka project has created the Streams toolkit for creating back-pressured, asynchronous stream processors. Diagramming them out can be quite common, and this stencil is designed to help you do that.
UML2
The UML2 activity diagram notation is an OMG standard, focusing on describing the business logic within a software system. More information can be found at the official website: http://www.uml.org.
Glycolysis
Glycolysis pathway: structures and names of intermediates, and coenzymes. The end product of glycolysis is pyruvate, but a reaction generating lactate is also included.
Nucl-AA
Stencil for nucleotide and amino acid residues. Open symbols.
Military Symbols II
This is the second of two stencils of military (NATO) symbols I made and use for my wargames maps and orders of battle. I created it by scanning an existing chart and then converting it into vectors.
Juniper M and MX series stencils
Stencils for Juniper M and MX series routers. Sized for 19" racks, works well with RackElements
Web Sketch Social Media Badges
Social Media badges in a "sketch" style, for mocking up web UX designs. Includes: Twitter, Facebook, StumbleUpon, Delicious, Digg, Reddit, Linkedin, MySpace, FriendFeed, RSS, Flickr, Technorati, YouTube, Bebo, and Pinterest.