Two drives sounds much better than one drive for me as well as I hate to keep OS all together with storage. It’s painful to move data when the OS needed to be baselined.
Yes, it is a much better idea to have a boot drive and a storage drive than to keep everything all together. The WD Green drives are great as storage (I've got two 2TB in RAID 1 in my workstation, and 15 more 2TB in RAID-Z2 in my server) but they are way too slow for anything else.
If you can't afford a decent SSD (Intel X25-M G2, OCZ Vertex 2, etc.), check out the Hybrid Seagate Momentus XT. It's a 2.5" drive (like notebook computers use and the form factor of most SSDs) so you may need a mounting adapter to get it in your case (figure $8 at NewEgg). Most reviews show that while non-repeated sequential or random tests aren't any faster than any other 7200 RPM disk, the 4GB SLC flash on board does an excellent job of caching frequently-accessed data, making real-world usage smoother. The power consumption will also be significantly lower than an additional 3.5" drive.


