MSc vs. BSc admission GPA for an application to a PhD program I am currently attending a BSc in CS from a research university. I should end up with a MSc in Software Verification.
I wish to apply to a research university in EU, UK, or Switzerland, for a PhD, later on, (really interested in Oxford, since they have a research group that could turn on as a natural progression to my master's course, in alternative, I am interested in EPFL or in ETH's Computer Systems group) since I am interested in doing research and applied research in the future (I am already reading some papers from these Universities to have my ideas straight).

The research areas I'm interested in are: Computer Systems (OS, Distributed Systems), Software Verification, Compilers.

However, probably my master's grades will be actually much better than my BSc grades. That said, my BSc grades won't be low, but they won't be top 0,1% either. My question is: From your experience, is the MSc GPA valued more or less than the BSc GPA for a PhD admission?
Typically, grades in undergraduate work are weighted more heavily than grades in graduate work. This is because your graduate work in general is focused on the research you do and the papers you publish as opposed to merely classwork. However, this is not to say that the answer to your question is clearly black or white. Indeed, any reasonable school will look at all aspects of the applicants (grades in both undergrad and beyond, summer projects, research experience, letters of recommendation, etc) when deciding if they are a good fit for their program. There are no doubt countless examples of students whose grades differed from the other applicants, but were accepted anyway. 

That being said, it's usually seen as a positive if your grades trend upwards near the end of undergraduate work and the beginning of graduate work. The idea is that if an applicant shows recent signs of improving, they (hopefully) are more likely to continue improving after joining the new program.

Finally, it's worth noting that different schools (and even different departments within a single school) handle their admissions process differently. As always with these types of specific questions, it's a good idea to ask the school's department directly about the matter. In particular, I'm sure that there's a contact in the CS department in Oxford you could email who could be able to answer this question directly.