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In my Master's thesis I have a lot of figures, tables, and code which is referenced in the text and should go into the appendix. Apart from that, I don't really know how to structure the appendix.

Should I create sections based on content (i.e. all figures into one section) or topic (based on table of contents)? Or is the choice up to me?

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I think that depends on how big your appendix is. If you have, say, only five items in your appendix, sectioning them would seem like an overkill. If you have fifty on the other hand, putting them into sections according to you thesis layout would seem fit. Usually they just get numbers like "A1", "A2", etc. regardless if it is a table, figure or something else.

Grouping by type of appendix item does not make any sense to me (tables, then figures, then raw data). Sorting should be according to the order the items are mentioned in the thesis.

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