What topics should go in the thesis Appendix?
If the methods that you are considering including in the appendix were necessary to arrive at your final results, then they certainly aren't "off topic". Without knowing your field of study or your topic of research, it's hard to give a more direct answer than that.

I'm in the social sciences, and we often include mathematical proofs in our appendices in order to save space in the main text (as well as not distract from the substance). Nonetheless, given the importance of transparency, we include our proofs for review by others.