Hi dugh,
wayoda/Eberhard, you're mistaken and conflating USB 2.0 with the arduino. USB 2.0 may give you 1000 reports per second, but not the arduino, even though it uses a USB connector. In the examples I've seen the arduino is much slower because of the usb to serial stuff.
Yes, you are right. In a forum you usually don't know how much background the other people reading the thread have.
I just wanted to point out, that even NI is not able to do a live-stream of data at 10ksamples/s.
Now back to the arduino:
Take for example an arduino-based mouse. It would jump around when you move the mouse fast because the serial port connection isn't fast enough to handle smooth mouse movement.
I really don't know the maximum timespan for the "mental" delay between a body-movement and the feedback on a computer screen.
I know it's 20ms with musical issues. That is the time between hitting a key on an instrument and the sound from the speaker coming back to your ears. If is <=20ms you don't have a feeling of delay. Daniel Barenboim might have a different opinon on this 
A software that generates screen-updates at 100 fps leaves you with a maximum of 10 ms between two new images on your eyes. I think the Arduino should be able to send at least 2 ints for the relative mouse movement during these 10 ms. I didn't try but this should be possible...
The guy who made the arduino logic analyzer also points out issues with the sampling rate. "I really need to move it off Arduino and do the interrupt servicing in assembly. It's far too slow for what it's supposed to do."
This is not a problem with interfacing from the desktop to the Arduino. It is simply a question of choosing the right tool for a project. If the Arduino-Language is too slow, you have to move to assembly....
This is a first step if it ever gets off the ground, making arduino HID compatible:
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1172471904
or the effort to use avr-usb for interfacing with the arduino:
http://www.obdev.at/products/avrusb/index.html
I don't think that any one of these efforts will give more that USB 1.1 low-speed (~750 Bytes/s) throughput. The Arduino/FTDI can easily compete with that.
If you need something faster you'll have to go for a dedicated piece of hardware. There are USB-chips available that run at 12MBit and implement SPI- and IIC-interfaces in hardware. But a single chip is more expensive than a fully assembled Arduino.
I would really like to have a USB-Arduino with a dedicated Vendor-Id/Product-Id/SerialNumber that says
"Hi, I'm an Arduino HID-Device and since my serial-number is 12345678, I'm the on that operates your coffe-machine. What can I do for you?"
Instead of
"Hi, I'm a USB-Serial-device and probably an Arduino too! "
"Can I get a cappucino please?"
"No, sorry I'm a modem ;-)"
Eberhard