How to measure the agreement between to curves?
If the signals are not aligned, yet you have a clue that they more or less "mean" the same thing, or refer to similar data, you could use dynamic time warping (DTW) algorithm to obtain a better correspondence (then simply taking the value at the same location). You could measure RMS, MSE or whatever you like, using those correspondences. For DTW, you might want to check:
http://en.wikipedia.org/wiki/Dynamic_time_warping

A good way to elaborate this idea is utilized in Earth Mover Distance (EMD), which computes the minimal effort to bring the signals to alignment, as a distance measure. EMD is presented here:
http://ai.stanford.edu/~rubner/emd/default.htm

EMD gives you a direct distance, which you might use for further analysis.