Begining with 1.3.2, skim migrated to a more advanced build system bksys (http://freehackers.org/~tnagy/bksys.html) 

Install is simple, just
./configure
./scons
./scons install

A prefix can be passed to configure as follows:
./configure prefix=/usr

DESTDIR is also supported in the install process 
./scons install DESTDIR=/tmp/blah

use ./configure --help to have a list of available options

Uninstall:
./scons -c install

Notice:
 * When you want to recompile your skim, please make sure to do this first to clean the source tree and caches
   ./scons -c && rm cache -fr
 * If you have scons install already, you still have to use the bundled scons: it is a patched version to support soft links
 * Please delete the file ~/.kde/share/apps/skim/mainwindowui.rc if you upgrade from skim <= 1.3.0

More details: http://scim.sf.net or http://www.scim-im.org