Hi ustacp,
You ask a very interesting question about which OS has a better file system. However, you limit the domain to either Linux or Microsoft (I presume you mean NTFS or M$'s as yet unreleased FS which was to make its debut in Vista but didn't).
As near as Unix and Linux are while they do share some commonality, they can have different file systems. Unix has been around a longer time than either Linux or M$ OSes and as such is the most mature.
In order to understand the meaning of "better" it is necessary to introduce one or more metrics by which "better" can be evaluated. Here are several well-known metrics: performance {size, search, backup, recovery}, reliability {journaled or not, stability}, features {ease of use vs expertise to use, ease of creation and destruction, ease of expansion and shrinking, security, user control}.
First, let me say - I am biased, particularly away from M$. First, they need to design a system to be secure from scratch (which they may have done? I am unsure about this - internal code named Singularity), but since it is a research OS (they remarkably designed and built a new language in which to encode it), however, they are likely never to bring it to market. The reason is that they probably have a lack of motivation due to the fact that the OS is not coupled to the interfaces in which all of the M$ applications are written and would severely put a dent in their revenue and those of 3rd party application vendors.
Now, with regard to M$ security, the most critical mistake they have made and continue to make (IMO) is to have the idea of a Registry - which is the single most unreliable mechanism to be available to any piece of software that a user can install - part of the problem is that users of M$ systems are not wise to avoiding common security mistakes - the Internet is full of predatory malware hunting for the unwary user.
That is the backdrop and basis for my POV with regard to taking a stab at answering your question, however, I do not consider it an answer to your question - particularly since my bias gets in the way of giving you a straightforward easily digestible answer that is both fair and impartial in answering your question.
I am sure there may be published Reviews considering your question, and at this point the best I can suggest is to look for them - but, where?
I would start with a search for: file system comparison +Linux +Windows
in several different search engines to see what you come up with. Here is a list of suggested search engines: Google, AltaVista, Yahoo, Dogpile, Answers, Mamma.
Here is the first link I came up with using Yahoo at Wikipedia
here.
It looks like a good place to start, but the really crucial question you have to ask yourself is what your needs are - i.e. what is the major application you need that a particular file system fits well in order to answer your question, OS aside.
Note: Beware the neutrality of the articles you find.
-- Tom