I've done a lot of research on the best possible way to partition my hard disks and I think my partitions are working wonderfully right now. I have little fragmentation and the file access time is less. My computer is now almost 2 years old and still works like a charm (although I have added a HDD and 1GB extra ram since I bought it).

Here are the main points that you need to keep in mind while partitioning you hard disk:

1)If you have more than 1 hard disk then partition them in such a way so that both the hard disks get to work simultaneously. Since both hard disks will be working together, they will get work done in lesser time. Even in an one hard disk system try to work on multiple partitions at a time.

2)Make sure you identify which partitions would contain variable amounts of data and the ones which will, more or less, contain the same amount of data.

3)FAT32 is faster for partitions less than 10GBs

4)Cluster size: Larger clusters waste more space but generally provide for slightly better performance because there will be less fragmentation and more of the file will be in consecutive blocks.

Now here is what you can do to implement the above:

Keep a separate partition for the pagefile. Normally the size of this partition (your pagefile size) should be 1.5 times the amount of ram that you have also keep this size fixed.
This will also reduce fragmentation on your other partitions. You can format this partition using FAT32 as it will be less than 10GB and try to keep it on the hard disk which does not have your OS.
 
Keep a separate partition for Proram files and My Documents on the other hard disk than the one having your OS.This will result in a more or less fixed size for you OS, so install your OS on a 10-15 GB partition.

Keep a high cluster size for the partitions containing media files (2 KB or 4 KB) and enable ntfs compression. Ntfs compression lowers the performance a little bit so if you have plenty of free space don't use it.

Dynamic Disks:
Converting your Hard Disks to Dynamic Disks has some advantages like more options while partitioning like striped volumes and spanned volumes.A striped volume is basically a volume split over two hard disks and data distributed among these volumes in stripes so both the hard disks work while accessing the same data. This obviously has some speed benifit, however, it also has some serious negatives. You will not be able to access your hard disk from a different computer nor will you be able to install another operating system. 
You will have to format your entire hard disk if you want to go back to using a basic disk.

So just keep the above in mind while reformatting your hard disks and you can really speed up your system.

Man the tips are cool especially the one about the system pagefile. That should definitely speed things up.

If the hard disk will crash ,you can loose entire informations. So , have you tried to use two separate HDD ? I am using and i am feeling very comfortable .