In case you may find it useful, here's my HDD/SSD settings and partitioning. I'm sure my way doesn't suit everyone, but it works for me. I'm sure there's lots of equally good strategies out there.
Currently, I have a 60GB OCZ Vertex II SSD for the Operating System, a 300GB WD Velociraptor for Applications and Games, and a WD Black 1TB Drive for everything else. I've also got an external Seagate 1TB drive for backups of backups and for my wife to back things up to.
All drives are formatted NTFS unless otherwise specified. Also, all drives are set to AHCI mode in BIOS.
SSD has the 100MB partition that Windows 7 makes at the front, then a 46 GB primary partition for Windows. 9.8 GB is left unallocated for wear leveling, etc. (short stroking). I did this because on that particular drive, the 50GB version and 60GB version are exactly the same, except for the spare area. OCZ decided that they didn't need to leave so much spare area and changed the available size. On this drive, I only install the operating system, virus scan program and add-ons like Adobe Reader. I move my user profile to the 1 TB drive.
The Raptor has two partions, 180 GB for Games and 100 GB for Apps, both primary.
The WD Black 1 TB has 7 partitions:
1st partition is 50 GB Primary for User Profiles. You have to copy the default profile and change the registry among other things. Here's a link http://www.maximumpc.com/article/howtos/howto_optimize_your_windows_profile_and_media_storage_ssd
It's best to do this right when you install Windows to avoid extra legwork.
2nd partition is 16 GB Primary for the page file (virtual memory). Don't forget to move this off the SSD to avoid unnecessary reads/writes. I set the page file to 6GB to match the RAM I have. 16 GB is overkill, but I left it that big because I have the space and if I increase my RAM, I have some room to grow. In retrospect, I should have put this partition first before the User Profiles to take advantage of the fastest part of the disk.
3rd partition is 2 GB Primary Fat32 for Linux Swap File. I don't currently have Linux installed, but you never know. Linux requires a swap partition, so I put it here just in case.
4th partition is 150 GB Extended and I have called this Utility. I don't have plans for it yet, but I may use it for storage of video while video editing. I could also install Linux here. If I want to do both, I can delete it and divide it up.
5th partition is 450 GB Extended for Media. Pictures, videos, music go here.
6th partition is 125 GB Extended for Data. Here, I store downloaded install files, documents, etc.
7th partition is 138.5 GB Extended for backups. Here, I store Ghost images of the OS partition and User Profile partition. You have to take an image of both every time.
My 1 TB external is split into 7 partitions for various backups of files. I plan on making use of synctoy for this in the future, but haven't done much with it yet.
All that said, I just pulled the trigger on a 120 GB Intel 510 SSD using the 10% off newegg coupon I just got. I'm going to use this for Games and Apps I want to open quickly. The 300 GB Raptor is going to become space for other apps. I'm going to move the page file to a 16 GB first partition there as well.
Anyway, thought I'd share my partitioning strategy. Probably big time overkill for 99% of people, but that's how I roll. Hopefully, you can get something out of it.