In the master's program that I am enrolled in, there are two options before graduating: either to complete the thesis or to do a project. I thought of doing the thesis, and maybe if I can find a topic that can be continued for a PhD program, use it for my dissertation in the future. Most of my peers are opting for the project. My question is: does it matter in the long run what I do?
It depends on your goal (and, to a degree, your subject area). If your goal is to do a PhD and enter academia, you will most likely be better served by the thesis as it will most likely prepare you better for doctoral research and dissertation especially in terms of research design, qualitative and or quantitative methods, and understanding of the related academic literature in your field.
By contrast, if your goal is to go into industry, in many fields, you may be better served by doing a Master's project in collaboration with an industry partner such that your project work can be applied directly in practice. Your project work will improve your skills related to producing outputs that are valuable to your industry of focus and will help broaden your network of industry contacts which can be quite useful to your career.