Background and question
I often work with simulations of dynamical systems and I usually track a single parameter $x$, such as the number of agents (for agents based models) or the error rate (for neural networks). This parameter usually has some interesting transient behavior. The type and length of this behavior depends on the random seed and simulation parameters. However, after the initial transient period, the system stabilizes and has small (in comparison to the size of the changes in the transient period) thermal fluctuations $\sigma$ around some mean value $x^*$. This mean value, and the size of thermal fluctuations depends on the simulation parameters, but not on the random seed, and are not known ahead of time.
The goal is to have a good way to automatically stop the simulation once it has transitioned from the initial transient period to the long-term behavior. We know that this transition will only happen once, and the transient period will have much more volatile behavior than the stable state.
Naive approaches
The naive approach that first pops into my mind (which I have seen used as win conditions for some neural networks, for instance) is to pick to parameters $T$ and $E$, then if for the last $T$ timesteps there are not two points $x$ and $x'$ such that $x' - x > E$ then we conclude we have stabilized. This approach is easy, but not very rigorous. It also forces me to guess at what good values of $T$ and $E$ should be.
Alternatively we can use a time $T$ and confidence parameter $\alpha$ as in this answer and assume a normal distribution on the error. This will save us the effort of knowing the size of thermal fluctuations.
Let $y_t = x_{t + 1} - x_{t}$ be the change in the time series between timestep $t$ and $t + 1$. When the series is stable around $x^*$, $y$ will fluctuate around zero with some standard error. Take the last $T$, $y_t$'s and fit a Gaussian with confidence $\alpha$ using a function like Matlab's normfit. The fit will give us a mean $\mu$ with $\alpha$ confidence error on the mean $E_\mu$ and a standard deviation $\sigma$ with corresponding error $E_\sigma$. If $0 \in (\mu - E_\mu, \mu + E_\mu)$, then you can accept. If you want to be extra sure, then you can also renormalize the $y_t$s by the $\sigma$ you found (so that you now have standard deviation $1$) and test with the Kolmogorov-Smirnov test at the $\alpha$ confidence level, or one of the other strategies in this question.
Notes
This question was originally posted to Cross Validated in a more time-series centered language. It generated some good discussion, but not an answer I was happy with. I tried MetaOptimize but the question generated zero interest there. I am not familiar with the tagging on Computational Science, so feel free to edit the tags.