Locating OS and applications/games onto separate physical disks is the way to go for maximum performance, especially when using SCSI/SAS/SATA disks, all of which provide simultaneous access to multiple disks. Most apps, especially large, expensive one like Office/Photoshop will pound both disks heavily and achieve a very noticeable performance gain, especially when starting.
However, I strongly discourage moving the "Program Files" or any other default path other than "My [Documents|Pictures]." Moving the other defaults will result in a nasty mess of duplicated, orphaned, dependent, and/or unmovable files in the original and modified locations, as well as happy fellow up the organization of your user profile paths.
The most convenient and problem-free scheme is to just leave "Program Files" set on C:, and create another "Program Files" directory in the root of your designated Programs partition. When you install an application, simply change the drive letter from C: to the letter for you Programs partition.
Sloppy apps that force themselves to C:\Program Files\ can still get there, and those that split themselves between your choice and C:\Program Files\ (such as the aforementioned Office & Photoshop) may even benefit from further increase in potential parallelization.
I personally dislike the "My [Documents|Pictures]" trees, as I prefer to create my own top-level directories in the root of my Data partition, which is where I also move the "My [Documents|Pictures]" trees for those applications lacking the courtesy to ask where I want my data. Fortunately, those programs are few and far between.
Keeping most of your data on a separate partition will reduce fragmentation and areal stratification of OS files, allow for a smaller, faster OS partition, ease backups and OS reinstallation, and improve the efficacy of the Windows Prefetcher. Just make sure you make the OS partition large enough to accommodate application files that demand residing there. 4-6GB was fine for me in Win2K... I just started using WinXP x64, and 16GB seems about right so far, maybe 24GB in the end.
Placing your Data partition after your OS partition is also a smart move... Once your app loads files it needs from the OS partition into RAM, you can now work with your data files and your application will be free to access task-specific files from your Programs partition simultaneously.
As for pagefiles, I recommend setting them to a fixed size, and following MS's recommendation by placing one on each physical disk. Windows automatically shifts paging activity to the drive(s) experiencing the lowest utilization.
This is my Windows partitioning scheme that I've been fine-tuning since Win2K was released, making improvements based on data provided by Windows Performance Monitor to get the best performance by minimizing disk contention, and maximizing parallelization, throughput, and convenience, without compromising compatibility or reliability.