putting stuff on the root-partition (or system partition when talking windows) isnt something i would feel comfortable doing.
i mean, even in windows i strictly keep my windows-partition free of anything not windows-related, although its not necessarely needed in windows.

thats why i asked if you can tell beforehand where a program is going to install itself. or consequently, if its possible to clean the system-partition from non-system programs if they installed themself to that location (will a simple uninstall of a program delete everything?).
or if you can customize the install-location, even though it seems that in linux these locations are pre-determined.