First thing first: BACKUP your data to separate, independent, hard disk.
As stated above, using a Live CD distribution of Linux is perhaps the best way to salvage your data. I did this in the past to rescue data for my Brother-in-law, using Knoppix, back then. But Ubuntu can also do the job. The key thing here is to first understand the disks that you currently have in your computer, and their partition.
Firs thing to do is to boot form a live CD distro, and look at what is currently mounted. Under Ubuntu, the other internal hard disks partition may not be automounted, but will remain available, being mounted after confirmation.
Then, and only then, plug in an external, portable hard disk that you would have first prepared using another computer/laptop. Although Linux can now handle NTFS partitions, I would recommend to use FAT32 ones for now. I also found that FAT32 partitions made by Ubuntu may be unreadable by Windows itself, so be careful on how you make this.
Under Linux, partitions are seen as names such as /dev/sdb1, for example. Ant they are mounted to sub-directories from the main one, not drive letters.
If you are not familiar with Linux, try to find someone who is, in your area. Better safe than sorry, even if you have to pay few bucks.
THEN, re-install your Windows on your first partition. again, be sure you select the right partition when re-installing it. It is recommended to manually specify the partition. The automatic way could re-allocate the entire hard disk and destroy all partitions.
Once your base Windows is re-installed, check that you can access the secondary partition, which should come up as drive D:, usually. Then, re-install the other software, drivers, etc.....
IF anything goes wrong, you have your backup on the external disk.
NOW, the secondary disk may be fragmented, and re-formatting and restoring the data will give you back a speedy hard disk which can improve your performance, but this is a bonus, not needed to get back in business. Most of the defragmenting software out there will only do a partial job.