Uninstalling files installed with make can be troublesome. The first thing to check would be if there is an uninstall option in the Makefile for the particular application. Failing that, look at the Makefile to determine what and where it installed. One thing you can do to help minimize non-rpm based headaches is to always install in /usr/local. Most rpms will install in /usr by default, and /usr/local should be lower on the prioriy list for execution paths.
Also, try to find an rpm if possible (obviously). If there is an rpm available, but it is older and out of date, you might be able to make the new software available through rpm by installing the older program's src.rpm, and updating the <program>.spec file to use the new source code. Failing that, you could possibly make an rpm by following the spec file from a similar application (say unrar for example). Check one of the yast repositories