What is the best lower bound for the fault-tolerance threshold in quantum computing?
The highest threshold lower bound for for independent stochastic noise of which I am aware is $1.04 \times 10^{-3}$ by Aliferis, Gottesman and Preskill (quant-ph/0703264).  They analyze Knill's teleportation-based scheme with postselection.

If you are willing to consider independent depolarizing noise, then I know of two slightly higher lower bounds: $1.25\times 10^{-3}$ by Aliferis and Preskill (arXiv:0809.5063) and $1.32 \times 10^{-3}$ by myself and Ben Reichardt (arXiv:1106.2190).