What license to choose for my PhD thesis?
CC-BY seems to be the industry standard license for open access papers, see Why CC-BY? for a discussion of the reasons. It's a well-known license, that allows various kinds of later use (including commercial), and hence it's a good choice for papers and (I think) theses as well. The BY part requires "appropriate attribution". For academic reuse you can pretty much count on the attribution coming in the form of citations.

Note, however, that CC-BY is not a "viral" license. That is, modifications don't have to preserve the license. If you want that property, there is the CC-BY-SA (share-alike) variant, but my understanding is that it can make it problematic to create repositories of documents. This is one of the reasons for recommending CC-BY for papers. However, you could always put a CC-BY license on the thesis, and a stricter one on the helper tools.

Just make sure that whatever you choose is compatible with any copyright policy imposed by your university. Places I'm familiar with just request non-exclusive distribution rights to put it in their online library databases, but I imagine other places can be more restrictive.