newegg no longer sells them.

are they still making them, with all the bells and whistles like usb 3.0 front ports?

Here's one brand, but the models seem old, dunno if you can find them in stock.

http://www.sunbeamtech.com/PRODUCTS/Acrylic/Acrylic.htm

Nowadays they are mostly limited to open bench/test bed and watercooling specialties (pricey), but you can still order regular ATX towers from Asia on the aliexpress.com platform (although there should be a small selection on Xoxide.com).

they support modern features like USB 3.0?

i love light sabers.

IMO a clear case with CCFL or LED lights is like light sabers.

beautiful

the sad thing though is that AFAIK seasonic fanless and other high quality PSU aren't made in clear case.

IMO a clear case with ccfl/led with a clear PSU and lots of LED and a christmas LED tree heat pipe cooler
and clear DVD burner

beautiful

In fact they are making them but they are way to overpriced for common buyer.

Custom made acrylic case are a little cheaper, but you need to make an effort to build it like i did:
viewtopic.php?f=15&t=67099
or
viewtopic.php?f=15&t=68211

Assuming that you need something more serious than internet/office machine, try Parvum cases. They seem to be well made:
http://www.parvumsystems.com/

If you like to customize every inch of your case and pay less for it, make it your own case like i will.

@dan
Cases made by transparent plexiglass are good because they show hardware which most of people like to see and admire.
Bad side of transparent cases are cables and dust.
No one wants to see bunch of tangled cables and even beautiful piece of hardware covered with dust.

Every so often see-thru cases come back but they don't last long. My take is, seeing the innards is only interesting to the builder, and not for long, after a while it feels like a toy, than a serious, cost you a $grand to build.