Software(programs) can be installed in any accessable partition and run fine...
A personal choice where ya keep em...
A sorta conventional setup to put the OS and Primary(or critical) software(like anti- virus, office, acrobat, SQL Server, media players, burn software, etc) on the system partition. Usually if there is a requirement that the software MUST reside on the system partition it will tell ya so and just wont install anywhere else...
For accessory stuff( like Audio catalyst, Clip'nSav, WinZip, WinAmp) put em anyplace ya want. Personally, I keep stuff that I've downloaded and installed on non system partitions, and stuff I have CD source for on system partitions. It makes it simple, upgrade the OS and ya dont have to go find WinZip download again... But feel free to roll your own for personal convieience and organization here...
Most important is to keep DATA off the system drive.. Like change the default location of Word docs, SpreadSheets, Music/MP3's, source zip packages and downloaded software... Then all ya have to do to upgrade/replace the os is drag a couple of needed files(like your email repository, ie: outlook.pst) off the system partion and then format/install all ya want... your DATA is on another partition...
The rules are: A much as possible - Make it easy on yourself!
(and keep those source zip downloads of required drivers off the system partition also - they come in real handy for reinstalls also)