Autocorrelations: Measure the autocorrelation time over the whole simulation, and then throw away data for at least the first sweeps.
Hot and cold starts: Start from hot (random) configuration and also a cold (ordered) configuration. When the two have converged to the same results, then the system is equilibrated. (But what about first order phase transitions at ? Usually will not get convergence --- in fact this is a good way to look for first order transitions.)