Paul over at Dorkbotpdx has written a detailed article on his USB virtual serial receive speed benchmarks:
As part of optimization work to support large-scale LED projects, PJRC developed three simple USB virtual serial receive speed benchmarks. The complete source code is available below.
Here are the benchmark results for boards that currently support native USB virtual serial for Arduino sketches. These tests show the importance of efficient USB software. The actual speed a board achieves depends much more on its software design than its raw hardware speed.