Let me lay out my methodology for testing wired Ethernet speed, and other concerns, mainly unforeseen bottlenecks. Then I will propose scenarios for benchmarking USB speeds on the PI2.
Let me know if there are any issues.
First: Benchmarking wired Ethernet of the PI2
I will build a Raspian (Debian Wheezy, current version) image and shut down all unnecessary processes. It will be headless and Samba Server installed. No interaction with the PI will be needed other than accessing the share externally.
It will be connected to a port on a Cisco switch hard coded to speed 100, duplex full. The switch will have SNMP turned on and a polling workstation will poll the PI2's switch port for throughput measurements at one second intervals. Polling of the switch port data will not effect the PI as you are really polling the switch's CPU. SNMP polling of a Cisco switch has a negligible effect.
A reference file will be selected of 500MB to 1GB in size. It all depends, I don't want the transfer to end too quickly. Multiple copies of this file will be placed on the PI's CIFS share named File1, File2, File3, File4 etc.... CIFS overhead is not a factor as any overhead will be part of the measurements. CIFS overhead would be a factor in any type of timed transfer scenario. One client workstation will pull File1 from the share, a second client workstation will pull File2 and so on. Maximum outbound throughput will be considered reached when an additional client workstation pull does not increase observed bandwidth utilization.
A similar test will be performed by the client workstations pushing the file to the share.
The true upload and download speeds of the wired Ethernet will then be observed on the graphs produced by the polling software.
One concern I thought of with this scenario is the performance of the microSD card.
I will be using this one:

it is the SanDisk SDSDQUAN-016G-G4A. Here is a note from their website:
"Up to 48MB/s read speed; write speed lower. Based on internal testing; performance may be lower depending on host device, interface, usage conditions and other factors. 1MB=1,000,000 bytes."
That works out to 384 Megabits per second read speed under ideal conditions, but no posted write speeds.
If the bandwidth for file push is way lower than file pull microSD write speed may be at fault.
Let me know if there is a better card out there please.
Second: Benchmarking of True USB Bus speed.
My first thought was to use the same methodology as above using this:
It is a Gigabit Ethernet USB 2.0 adapter with Linux support. But then I thought about the theoretical maximum speed of the microSD as published is 384Mbps whereas theoretical USB max is 480Mbps.
In this case the microSD would be a theoretical bottleneck. Then updatelee mentioned dd to an external drive which would remove any microSD bottlenecks from the equation, especially when there are no published write speeds.
Taking UDL's advice I found this article:
http://www.binarytides.com/linux-test-drive-speed/
"USB 2.0 has a theoretical maximum signaling rate of 480 Mbits/s or 60 Mbytes/s. However due to various constraints the maximum throughput is restricted to around 280 Mbit/s or 35 Mbytes/s. Beyond this the actual speed achieved depends on the quality of the pen drives and other factors too."
Here's another:
http://raspberrypi.stackexchange.com/questions/4268/benchmark-usb-hdd
My only issue is what device to use as the test subject? I don't have anything on hand good enough.
You really want to test a device where the bottle neck is usb bus speed and not read/write times of the media itself.
Is there someone else that can run the USB test using dd?
If not I can try the Gig Ethernet adapter.
So the equation
(Measured USB Max Speed) - (Measured Ethernet Max Speed) should give us the remaining throughput left over on the USB bus for a tuner.