Other Parts Discussed in Post: TUSB7340, TUSB8040
First, I wanted to tell everyone how exciting it was last week at the USB-IF Compliance workshop to see so many SuperSpeed USB end-products there for certification - it was a thing of beauty!  Of course there were silicon suppliers as well including us doing testing for our TUSB8040, SuperSpeed HUB, and TUSB7340, SuperSpeed Host controller.
Now on to the topic of the day - What is the real throughput that one can expect over a SuperSpeed USB link?
First, we need to understand that 8b/10b encoding is used in the data transmission, so while the raw bit rate is 5 Gbps, the encoding cuts this down by 20% to 4 Gbps. For those of you who are Firewire (IEEE-1394) fans, the lower number is actually the way the 1394b speeds are defined: s800 is actually a raw 1Gbps bit rate, s1600 is 2 Gbps raw bit rate, and s3200 is 4Gbps raw bit rate.
The next factor is the overhead of headers, etc. For examples, in one benchmark test, we have run our TUSB9260 (USB-to-SATA) talking to a solid-state drive (SSD) and are seeing 252.4 MBps of read throughput.  If you take that exact same SSD and connect it directly to the SATA host in the same PC, the throughput is 258.2 MBps.  This means that the USB "overhead" is roughly 6 MBps - every time you run the benchmark, you get slightly different results, so I took the best of five trials for each. This means the USB overhead is roughly 2% of the total bandwidth.  This would reduce the overall 4Gbps down to right around 3.9Gbps (~485 MBps) range.
The much bigger issue is the software that is needed on the PC/DSP to process the data.  For example, with the new USB Attached SCSI Protocol Mass Storage driver running on a high-end processor PC with an advanced 6-Gig Serial ATA drive, the expectations are that the throughput for reads from the drive to the PC will max out in the 350 MBps range (~2.8Gbps).  But this is an ideal world and we are seeing more in the 300 MBps (~2.4 Gbps) range for normal implementations.
Please let me know what applications you are working on that take advantage of the throughput of SuperSpeed USB that you could NOT do with USB 2.0!