I beg to differ. >6" height shelves in TV-related stands are not common, imo.
So many models have adjustable shelf height or removable shelves. I can understand people who are trying to fit something new into an old school entertainment center having an issue, but if you are looking to buy something right now, there is no reason for it to be. Anyway, my point is that there are tangible benefits (better component choice) for greater height; so I'd rather try and accommodate it over greater depth. Optimally, you could get everything you wanted integrated onto a m-ITX package at a good price and this wouldn't be an issue, but we aren't there yet.
And those monster AVRs are difficult to house.
That's why I said if you have one the size of your HTPC case is probably irrelevant.
I bought a cheap 5' wide TV stand from Ikea (under $100 iirc) for my 40" panel TV. It is typical -- it stands 14" tall and has one shelf that spans the width. The shelf is 6" tall and 21" deep.
I think the stand you bought is far from a common choice. $100 is very cheap for this sort of thing. Also, I'm not surprised something 5' wide is fairly deep. The only people who need
a 5' wide stand are those with giant DLP that are also 18" or more deep. Your 40" panel TV is so light that it has no need of such a bulky stand. You could likely gotten away with something that isn't even the full width of the TV.
My point is why do you want to use a stand that is 21" deep with a panel TV? You can barely even buy a DLP TV that is deeper than 18" these days. I find most TV stands are now in the range of 12-18" depth. The style is for everything to be lower profile. Panel TV, panel speakers, low profile DVD players. Why are HTPC cases largely bucking this trend? The only one I can think of that is on the right track is the Silverstone GD02 (6" high, 14" deep) and it has some strange design quirks and a relatively high price.