if you would like to analyze the stability of a process, e.g. number of events per experiment, which is a time series it is probably interesting to use an Allan Variance:
This is widely used in the domain of frequency measurements or clock characterization.
If you are dealing with proportions, you must first transform your data using compositional data analysis techniques. This assures that the analysis does not depend on units, on the definition of the total sum of proportions and that you will not have to interpret proportions greater than 100% or lower than 0%. Then you can freely apply time series techniques across your transformed data. This paper may guide you in the process.
As for the tools, I suggest the use of R. There are some packages that offer functions to deal with proportions, namely in the "compositions" package. This package is thoroughly described in the book "Analyzing compositional data with R" (Springer). As for time series, R includes some functions, but you might have a look at the "forecast" package.