There are several tools all built around Xperf. It's rather complex but very powerful -- see the quick start guide. There are other useful resources on the Windows Performance Analysis page
Here is a pretty intersting article, I don't know if it hits the target you are looking for but I think you may find it leading you in the direction you want.
For programmatically enforcing system call policies, you could use the same underlying engines as drstrace: the DynamoRIO tool platform (http://dynamorio.org) and the DrSyscall system call monitoring library (http://drmemory.org/docs/page_drsyscall.html). These use dynamic binary translation technology, which does incur some overhead (20%-30% in steady state, but much higher when running new code such as launching a big desktop app), which may or may not be suitable for your purposes.
strace is one of the few Cygwin programs that does not rely on the Cygwin DLL,
so you should be able to just copy strace.exe to where you want and use it.
You can use process monitor written by Mark Russinovich. This is a fantastic little application that will allow you to attach to any running process on the system and see all of the system calls that process is currently making.