You can make use of Managed GDI+ Methods to perform this task. Take a loot at the following CP article
Comparing Images using GDI+
Here are a few more reference links:
Image Processing Technique
Comparison Method 2
About Image Comparison :
Every Image has 2 most important and popular quantity. The Root Mean Square ( RMS ) and Signal to Noice Ratio ( SNR ) these are mere pixel ratio comparisons. Which dont really yield you the actual results.
You can make use of some advanced techniques as mentioned by @orc, or there is one more advanced and an entirely different approach to solve the problem. Which makes use of Frequency domain analysis allowing the measurement of minute distortion regardless of Translation.
You might take a look at those algorithms before you start implementing your solutions