The problem of the "case" for portable DIY project...

I've recently come across a problem that involves those who are building a portable electronic device like me: the case.
I'm working on a FPGA-base portable video HDMI recorder, and I'd like to find as soon as possible a case to protect the
board from accidental hits, external powder, and stuff. I could even "defintively" enclose the board into a case and program
it from the outside (with minimal physical access to board just to plug in the JTAG cable..).
now, speaking about my particular board (Diligent Atlys), what parameters should I take into consideration when choosing a case?
how much important is the right material, the shape; could the external case have an impact on overheating?

And.. what about the commercial plastic box the Atlys board came with? It is easy to make some holes through it for cables and I think it
would be better than no case at all...

One criterion that comes to mind is preventing static charge. Certain plastics may generate static more easily than others. You'll need a static charge detector to know the story in this regard.

Radio Shack did (or does) sell a variety of enclosures. Convenient though not cheap.

Consider the plastic boxes (organizers) carried by hardware / fishing / office supply.

The boxes that pills/ cosmetics/ air-fresheners come in.

To get a vented enclosure, consider picking up a used vcr. Common at yard sales and thrift shops.

For a while I was getting Nutrilite vitamins in green translucent plastic boxes, with a latching lid. These were ideal to put several of my projects in.

Today I defintively gave up the idea of using the plastic case of my Atlys board as "definitive" enclosure: made some tests and found that distance between board and external borders is too short to safely hold the connectors...no matter how I try to place it in the box: my videorecorder handles 6 cables in total (Power, HDMI in, HDMI out,UART, Ethernet, JTAG ).... so side "North" and "West" of Atlys will have the connectors attached: there is simply not enough space...

But I had an idea: what about building a homemade fiberglass box? The material is cheap and robust, and I could have the size and shape I want... has anyone tried fiberglass for creating a PCB enclosure?

Unless you've used fiberglass before, it may be tricky to pick up first time (are you talking about raw fiberglass
and bottles of epoxy?). You'd need to make a mold first. For many development boards, we used to just use
cut perspex to the size of the PCB, to shield the top and bottom, (it doesn't protect the sides) and use hex spacers
with screws to make the PCB sandwich.
I think many people do this approach for development boards, it is quite common.
If you really do need the sides protected, and really do need a custom sized box, then
maybe sides of perspex could be glued to the top and bottom perspex (maybe using modelers [toy aeroplane]
cement type adhesive? - I've never tried it), or you can get very tiny threaded screws that would be thinner
than the thickness of the perspex, if you can tap a thread into it successfully without cracking it.
A nicer plastic is Delrin if you have access to a machine shop. Then, it's possible to create any shape enclosure since
delrin is available in extremely thick chunks. Of course, then you need access to a machine and an expert.
Another approach (full of ideas today) could be a metal enclosure if you can cut (say) brass or aluminium sheet.
Maybe it can be brazed (I only ever did this once a very long time ago, and I don't know which metals can be
brazed, or how tidy it would be possible. Of course there is laser cutting but it's too expensive to be worth it
(I've done it a couple of times - not for a case). You get a extremely nice edge finish on acrylic sheet with a laser.

Now I understand your project is larger than the enclosures I suggested. You want something that looks professional.

At a thrift (second-hand) shop you might find an attache case or similar sturdy luggage.

Or a case for heavy expensive items (such as a power tool).

A rugged case to carry things in a truck, boat, etc.

A case with padding for heavy delicate items (such as china).

I found a "temporary"(?) solution: I bought a cheap plastic transparent box, made some holes on the bottom to hook my Atlys board, then used some steel wires to create some sort of "tunnels" so the cables could go through them without making pressure on the connectors; made some holes on the sides for the cables; everything looks firm now... JTAG programmer, hdmi in hdmi out, power, UART now all reside inside this portable box