I worked for a short time at the Australian equivalent of http://www.toollessplasticenclosures.com/
as a designer/troubleshooter and making up prototypes. It is a great technique for medium to large enclosures, but quite limited for smaller (handheld) ones. It also can look a bit dated design wise as curves are tricky. I see some pretty nice designs on the web gallery, but almost all are bench top or floor standing for high value (e.g. medical) devices.
As Romain mentioned, most OTS enclosure manufacturers (OKW, Hammond, etc) will do custom machining - which is great if they have a suitable enclosure to start with.
I often use 3D printed (FDM ABS) enclosures for various devices with specific form factors, such as animal trackers. I typically do the model in Geomagic, but plan to move to Fusion 360. After 3D printing we (my customer or I) coat the ABS with resin to provide extra strength and make it water tight. Admittedly the animals aren't too fussy about quality of finish
You can use a service like Shapeways or Protolabs to deliver those kinds of quantities with a production level (polished) finish in various materials. Both services have really neat on-line analysis tools where you upload your 3D model and it does a manufacturability analysis, giving almost immediate feedback on any problems with your model. I've had samples from Shapeways, and they're much more dimensionally accurate than my small 3D printer can manage, but I'm "restoring" a second hand 3D Systems Projet so I may be able to print much better resolution parts in-house soon.
For larger or more mechanically complex designs, I CNC parts out of sheet Aluminium, Acetal, HIPS, or Acrylic, and bend as needed. I could outsource this, but most of these devices are made very small quantity (<5 per year), so I do practically all the assembly in-house myself.