Design
MIT Professor Alex Slocum's ME/product design guide book
My greatest resource in completing MIT's mechanical engineering's first thermodynamics and fluids course was these notes from the MIT aero/astro department
Thousands of mechanisms, categorized and explained
How to design for resisting water ingress in harsh environments
Optics topics. Light guides, lenses, plastic optics, fiber optics, and more.
Resources compiled for MIT medical device design course, incl. GD&T, snap fits, prototyping ethos, and more.
A collection of strategic thinking models, from hype cycles to the BCG box
Manufacturing

Metal processes

Extensive details on manufacturing processes for metals, such as casting, forming, and drawing

Costs

CustomPartNet is great for getting ballpark numbers on part and tooling costs based on process and complexity

Compare material properties for your project
Check this when evaluating the suitability of a certain plastic for your application
Making stuff
Great place to start in choosing an adhesive.
MIT D-Lab's brief guide to adhesive selection
Electronics
Everything you wanted to know about batteries
How to design small speakers into consumer electronics