New Age Enclosures - They will usually send you free samples if you ask.
Teko Enclosures - Excellent quality, and very generous with samples. Fast, free shipping on all samples.
Stahlin Non-Metallic Enclosures - heavy-duty outdoor waterproof enclosures. PVC or fiberglass reinforced polyester. Some come with a completely transparent polycarbonate lid or a lid with a transparent polycarbonate viewing window.
Hammond Manufacturing - Versatile boxes, great service for adding custom machining to standard parts for moderate quantities. Transparent boxes make holes unnecessary for LED indicators, etc.
Envision Plastics & Design Uses NMR Technology (No Molds Required) to manufacture custom plastic enclosures for a variety of applications.
- The Electrical Wholesaler: splashproof boxes for bathrooms and kitchens, and weatherproof boxes for outside use.
- ip67 enclosures. www.aliexpress.com/ip67-enclosure_price.html
- Craig at Built-to-Spec put his design files for a BeagleBone enclosure on Thingiverse so anyone could make one from transparent acrylic with a laser cutter (or whatever color you want).
- Mike Doell designed a transparent plastic enclosure for Adafruit to hold a BeagleBone Black
- Pazdan makes enclosures milled out of solid aluminum for Adafruit to hold a BeagleBone Black
- Logic Supply designed an enclosure for the Beaglebone -- steel with orange or textured black paint.
- "beaglebone black" at thingiverse has many enclosure designs.
Raspberry Pi enclosure
- "Adafruit Pi Box - Enclosure for Raspberry Pi® Computers" (laser-cut acrylic case) (Is this the same as "Adafruit Pi Box - Enclosure for Raspberry Pi Model A or B"?
- Pi Plate Clip: an accessory that makes the Adafruit's Raspberry Pi Plate a little stronger.
- "Zebra VESA Mounting Plate for Raspberry Pi": fits the back of monitors that comply with the VESA standard 100mm, 75mm, or 50mm mounting holes.
- "Layer by Layer - Designing Raspberry Pi Zero 3D Printed Enclosure" -- does this tell how to customize the case?
- Pi-Top and pi-topCEED hold the Raspberry Pi and a LCD panel in an approximation of a laptop or desktop computer. 
According to a "Raspberry Pi Zero, Pi 2, B+, A+, Compute Module Dev Kit Comparison Chart", the PCBs themselves are:
- 85 mm x 56 mm : Raspberry Pi 2 Model B and B+
- 65 mm x 56 mm : Raspberry Pi 1 Model A+
- 65 mm x 30 mm : Raspberry Pi Compute Module
- 65 mm x 30 mm : Raspberry Pi Zero
- Dr. Patrick Hickey. "Space Station modular enclosures for Arduino & Raspberry Pi".
- "Clear Enclosure for Arduino"
- "Arduino Project Enclosure"
- "Dirt Cheap Arduino Enclosure"
working with foamcore
Edge of Space Sciences (EOSS) needs lightweight, well-insulated, and reasonably strong enclosures to (a) insulate the electronics package during transit through the cold ( -50 °F ) tropopause on its way to the stratosphere, and the more difficult job of (b) keep the recovery beacon operational after crash-landing on Earth.
The foamcore seemed to work best after EOSS flight tests with molded Styrofoam packaging material, built-up insulation-grade Styrofoam sheet, bulk closed-cell polyethylene foam, and foamcore sheet.
Mike Manes, W5VSI (and Doug Gentges ?) has written some tips on building EOSS enclosures out of foamcore and hot glue and a bit of Kapton tape: "Foamcore Payload Construction"; "Package Requirements"; "Foamcore Flight Experience"; "Foamcore Adhesives"; "Making Holes"; "Planning the Package".
working with acrylic
"DIY Acrylic Refugium" describes how to make an acrylic enclosure.