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.

Copyright only applies to the way ideas or information are presented, not the information itself. That's why you were able to just cite other researchers in your thesis without asking them. Therefore, you don't need to use any special license to make the information in your thesis usable by others, for any purpose at all.

The auxiliary files are more like software, so you can use either CC-BY-SA or GPL.

What license to choose for my PhD thesis?

Ask your PhD advisor. There could be legal constraints (e.g. imposed by some research grant contract funding your PhD work) you might not be aware of. But he/she certainly could redirect you to the knowledgeable persons (e.g. your University lawyers).

In Europe, for H2020 or HorizonEurope funded PhD work, some Open Content policy is required (e.g. at my CEA/LIST institution, it should be published under HAL).

As an European taxpayer I dislike the idea of increasing profit of ScienceDirect (probably mostly owned by american retirement funds) with the money I pay in taxes (most H2020 PhD work are 100% funded by the European Commission), so I approve such policies.

^{Alternatively, you or your advisor might not care at all about legal constraints. At Paris 6 University, they did -in practice- vary a lot from one year to the next one in the previous century, depending on the government directives given to the university rector}