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.
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.
"DIY Acrylic Refugium" describes how to make an acrylic enclosure.
Envision Plastics & Design Uses NMR Technology (No Molds Required) to manufacture custom plastic enclosures for a variety of applications.