LSLForge + Eclipse for anything that require multiple scripts. It becomes easy to manage projects, use common library, refactor, etc. And it's uptodate !
By enabling preprocessing on Phoenix, my inworld script is only 1 line like: #include "C:\SL\Script\MyScript1.lsl", getting directly the forged script without copy&paste.
Adding the Antenna plugin to Eclipse allows to use #ifdef directives aswell.
http://code.google.com/p/lslforge/
http://antenna.sourceforge.net/wtkpreprocess.php