When compiling application form source, being able to cleanly and easily uninstall is only capable if the developer added an uninstall target in the makefile. This will also require the source to be extracted when the need to uninstall arises. There is also the issue that is no record of what is installed or what version is installed.
[user@host ~]$ cd app [user@host app]$ ./configure && make && make install
CheckInstall can be used to convert source to a Debian, RPM, or Slackware package. It does this by running make install and tracking of every file modified using the installwatch utility. Then the package management system can be used to show what is installed and what version as well as uninstall the applications.