All
Interesting challenge this one... We need to build or buy some PC's that have multiple USB ports and NOT use HUBS.  We need UBS ports in multiples of 6.... and the extra ones for Keyboard/mouse/USB memory.
The PC has to be small - ultra small form factor OR could go 19" rack mounte.. but there is a catch there.
We found one USFF PC with 6 USB ports... and a PCIe expansion CARD...and it had one "COMBINED" PS2 port - but alas that does not allow true keyboard AND mourse operation.
Best would be TWO small form factor PC's that will sit flat within a 19" rack - have 8 ports onboard and a plug-in card for another 6 ports - so thats 14 - 2 for kbd/mouse and 12 for our application.
Another thought had been a 2u or possibly 3u rack mounted - an expansion cards for 24  (3 * 8 ??) USB ports.
USB 2 is good enough... USB 3 would be bonus.
Win 7 is ok - we know we can use XP.
Anyone got any ideas ?  We have searched most of the PC people we can think of and its not easy to get a clean solution.  If we get this right we will be ordering/making 10+ of these machines........Expansion Card is the only way possible, without designing a custom solution.
SFF with 7 ports:  http://www.newegg.com/Product/Product.aspx?Item=N82E16815158209&Tpk=usb%20card
I am getting to the same conclusion.......
We need USB ports in multiples of 6... so that card is good.....
Now comes the other idea........a PC that can support 3 or 4 of those cards and has enough USB ports of its own to support a 6-set for our application AND has USB for keyboard/mouse and being greedy at least a spare for USB memory sticks.....
24 ports for our app + 2 + 1 is great.............any more sets of 6 AND the kbd/mous/mem would be icing on cake.

I maybe should have added - 250-500GB HDD, 2-4GB memory, graphics is not a main driver as this is normal PC work (1280*1024), network card/DVD etc...Sorry

I did mean to say thanks to Computer_Commando !!!

24 USB ports needed total ? ?
They better be powered hubs...Many motherboard have 4, 2-PCI-e x 16 & 2-PCI-e x 1; you can use the x1 cards in an x16 slot.  4 slots, 4 cards, 4 USB buses w/7 ports each, not including the motherboard.  The cards linked to have power supply connectors, but you will have to get some adapters because most PSU's only have 1 or 2 mini-molex, you need 4, one for each card.  2 of these cables will do it.
http://www.newegg.com/Product/Product.aspx?Item=N82E16812296156

Can you tell us why & how many separate USB busses you require?  You said you need multiples of 6, but not how many multiples you need.  4 is maximum.Thanks again
The issue is that we are TRYING to build a multiway programmer station where each device we need to program needs to be on a unique USB.  We have tried a LOT of HUB solutions and the 1-2-1 mapping thru a HUB just does not seem to work.
The more devices we can connect per PC the better and cheaper the solution - as we have many many thousand devices to program.
The smaller the form factor PC the more portable the solution becomes.  We wanted to build a 1 PC and 4 off 6-way programmers... the docking station for the devices is a 6 way with 6 USB leads..
Some testing with the 12 USB setup we have got working has shown we will want 4GB to 6GB of memory.
The programming application is simple and does not need much in terms of graphics.....HDD space is going to be useful as we need to read, save, modify and write new data for each device and want to keep detailed records.....calculations show that a 500GB drive will allow at least 3 sets of complete programming  (thats over 100,000 devices) so thats ideal.  The reasons for looking at rack mounts is that we will have to transport this setup (well many setups as we are considering 10 to 20 of these) around the country and into some computer unfriendly environments..........
Hope this helpsAint gonna happen...
I think your strategy needs to be re-visited.
If it were that easy it would have been done 10 years ago.Not sure I follow you patio....
I have seen a number of USB cards that offer 6 additional ports. 
I believe you can get motherboards  that already have 6 or 8 ports....
So those 6/8 plus up to 3 * 6 cards means 24 or more ports....

I am seeking advice if my thoughts are correct or am missing something.........also anyone who has a good recommendation of a motherboard or alerady built PC that will cater for the 18 additional ports....

If I have made a big error here.. please point it out.

ThanksMotherboard with 6 PCI-e slots & 10 USB ports:  http://www.newegg.com/Product/Product.aspx?Item=N82E16813128532
You want us to design the whole system for you?  I've given you the motherboard, expansion cards, power cable; the rest is up to you.  I suspect you need the services of a hardware engineer.  You maybe making this more COMPLICATED than it needs to be.If you are building the device programmer then why not say have 128 devices to program with the same code and multiplex the usb data lines. Why have the pc controlling, powering, all those usb ports.
2 USB ports 1 for control of what chip/device is being programmed and 1 for data to the device currently being programmed.  Then you could use a laptop to program the devices.

If you can give more information I'm sure there is a different way to look at the problem instead of 6 usb cards.
Many thanks all..

The motherboard suggestions helped a lot and we have gone down that route.  Located a 2U chassis and motherboard with enough slots, found a 6-way USB card and all the other bits.
Had two companies suggest a build (warrenty) etc and one option of a self build.

We tested a 12 way setup - 2 of the cards - worked well.  Quick test of an expensive so-called "excellent" powered USB HUB and it failed... We susepct that the in-house application to do the programming has a real issue with HUBS....and I know I am not going to get the app changed in time.

So we are going for one of the 24 ways being built by a company..........

MANY thanks for all the help and adviceWhat kind of devices are you programming?