I want to change my current RAID (HDD based 4 sata 2 120GB) on which my OS (Windows 7) is installed to some more fancy fast and modern SSD based. I have 2 options - 4 OCZ AGT3-25SAT3-60G or one 120 GB OCZ RVD3-FHPX4-120G. What would show better speed for installed OS and apps performance? Would it still be faster if most of the data I work with is stored on some HDD's?
Your PCIE would probably be faster in the long hall since it will most likely support TRIM. Right now with RAID and SSDs, you will not get TRIM support *unless something has changed in the past few months.
TRIM will proactively delete files from the SSD since the data has to be deleted prior to rewriting.
There is far more to this comparison than just TRIM. PCIe is a much faster interface than SATA. You can see the spec for the RVD3-FHPX4-120G shows double max sequential read/write. IOPs are an order of magnitude higher. Unlike spinning disks, SSDs are more limited by interface bandwidth than the device itself. That said, there's no reason you couldn't manufacture an SSD that is much slower than the interface. You still need to look at the benchmarks. A plateau in the benchmark graphs can indicate bandwidth saturation on the interface.
There are a lot of ways to define 'faster'. Likely by any of these measures, the PCIe device will win. But, you need to define the problem more clearly and consider your objective. 60GB vs up to 480GB is very large capacity difference. You didn't mention what kind of RAID you're using, so you might be using anywhere from 120GB to 480GB. RAID (except RAID 0) provides redundancy, so this is usually more important to people than speed, when used.
TRIM is not something I have much familiarity with, but my current understanding is that the rcent Intel storage controllers allow a non-RAID device connected while in RAID mode to pass through TRIM. This does not mean a RAID array on the same setup will receive the TRIM commands. TRIM is currently under standardization by T13, so expect once it is standardized that it will have less compatibility restrictions.