A new function has been added to the codebase, and will be available in the next major release (T-0.3.3); smart upload rate fudging. Like many of my improvements, most people won't even notice it.
What is this feature? It accounts for "TCP ACK" overhead. Basically, when you download, your system sends acknowledgements for the data it's received back up the pipe. This isn't performed at the BitTorrent protocol level, but on a much lower level and the old codebase didn't take it into account. As a result, for people on asymmetric connections with 8X as fast downstream as up (1M/128K for example) or higher, setting your upload at 80% of your pipe's max would still result in upstream flooding at full download.
So what does this change? You will notice that your upload decreases a bit when you are downloading at full speed.
With the new client, it will be recommended you set your upload at 90% or higher of your pipe's max. This will mean better performance on start-up and when downloading without choking your upstream.