When you install OS X, you may see a new folder at the root of your boot drive called "Incompatible Software," which may contain a program file or perhaps a folder of program components. Granted the folder name itself is pretty self-explanatory about its contents, but if you see it after installing a new version of OS X on your system, then you might wonder what is going on.
While there always will be small bugs and other incompatibilities with various software packages when run on a newly released version of an operating system, there are some instances where developers and Apple have identified versions of programs that do not run properly on a specific version of OS X without an update, and may destabilize the system, resulting in crashes or the inability to boot properly.
Some of these programs may be self-contained application bundles that will appear as an APP file in the Incompatible Software folder, but others may be background scanners and security software, with components that may include PLIST files and other configuration files in separate folders.
In addition to putting things in the Incompatible Software folder, OS X may also simply prevent some known incompatible programs from opening, which may happen if you try to install one after having upgraded your version of OS X. Running such programs will result in a warning box instead of the program being allowed to execute.
If you see these items in the Incompatible Software folder, or any warnings when running programs, then contact the developer to see about installing an update or upgrade that is compatible with your version of OS X. If you purchased the program through the Mac App Store, then instead of contacting the developer you can visit its updates or Purchased sections to install the latest versions.
For any items in the Incompatible Software folder, you can simply remove them and the folder itself without harming the system in any way; Apple only keeps them around so you can have a reference as to what was removed.