Some huge (metaphysical?) questions I've been thinking about but which science has no answer to yet:
Why does matter exist? This is a different question from "Why does anything exist?" but it asks how is it in the universe that the original energy of the universe "congealed" into matter at all? What kept it from simply staying in energy form?
We know that much (most?) of the stuff in the universe is already in energy form, why didn't all of it stay that way? Or is it that all or most of the universe's energy did indeed become matter, but since it formed matter and anti-matter they came together and reformed the energy (or a new form of energy?) we see today?
Why do positive charges attract negative charges? Why do like charges repel? What does it even mean to be positively or negatively charged?
Relativity tells us that matter changes space-time to create the force of gravity we experience all the time. But how does this happen? How does matter alter space-time? What does that even mean?
These questions don't have any answers at this time. We are all so amazed at the progress we have made so far since the start of our Greek intellectual forebearers, but really it's just been a drop in the bucket for fundamental understanding of our universe.