You CANNOT legally clone/image an OEM installation of Windows if you attempt to customize it in any way. This is against the Microsoft licensing agreement. If you have ONE Volume License for the version of Windows you want to use, then you can build an image with that, customize it, and redeploy.
For example, you said you have 6 PCs. If all these PCs run Windows 7 Pro, you can buy 5 Windows 7 Pro Volume Licenses (minimum order -- unless you have a pre-existing recent Volume License agreement that enables you to order 1). and redeploy to all 6 machines. The point being, to be legal, you must use legally obtained Volume License media and a volume license key for a version that matches or is greater than the version that came pre-installed on the machines.
If you were using Windows server instead of Linux, deployment would be pretty easy using Windows Deployment Services (built in component of Windows 2003 and later Server editions).
So, to summarize and answer your two specific questions:
1.Can I clone them without losing the install partition?
Yes, but not if you customize them UNLESS you have a volume license copy of Win7
2.What is the best way to install 25 different software packages on these machines?
The BEST way is to build the machine, image, and deploy - but if you don't have the appropriate licenses, then you can install each machine fully one at a time or you can research each installation routine - SOME may be installable through script. But researching and testing this, while educational and MAY be beneficial in the long run, will take longer now.
Note: Microsoft has academic pricing and other offers you may be able to qualify for. In addition, you may qualify for purchases through TechSoup.org (or an equivalent organization -- I can't recall the name, but I know there's an equivalent org in Australia).