Here is a list of packages, present in both Salix and Slackware repositories and the reasons Salix is using a different build:

Salix 13.1

cups: Reverted back to version 1.4.3, but with security patches from version 1.4.4. Cups 1.4.4 makes all mozilla applications crash when printing if gnome-vfs is installed.
gst-plugins-good: The Slackware package has no support for using audio/video with a webcam.
libvorbis: Using the aotuv version instead, provides better quality encodes. Fully compatible with the official library version.
lilo: Slackware package repackaged with different artwork. Minor tweaks to liloconfig.
ntp: Altered scripts so it works out of the box.
pkgtools: The pkgtools package is available, but Salix is using spkg as default, however the original pkgtools are included even in the spkg-pkgtools package. Spkg is written in C and is much faster, see their website
sysvinit-scripts: Tweaked for boot speedup. Colorized boot messages. Autostart feature for every executable file in /etc/rc.d/.
hplip: No QT GUI.
wavpack: Newer version.
wpa_supplicant: No QT GUI.
xf86-video-intel: Offer both 2.11.0 and 2.9.1 versions of the driver. The older driver is needed for PCs with intel cards that fail to work with KMS with kernel 2.6.33.4.

Salix 13.0

libvorbis: Using the aotuv version instead, provides better quality encodes. Fully compatible with the official library version.
lilo: Slackware package repackaged with different artwork. Minor tweaks to liloconfig.
ntp: Altered scripts so it works out of the box.
pkgtools: The pkgtools package is available, but Salix is using spkg as default, however the original pkgtools are included even in the spkg-pkgtools package. Spkg is written in C and is much faster, see their website
shared-mime-info: Support for xz compressed files.
sysvinit-scripts: Some code added to support splashy at bootup. Autostart feature for every executable file in /etc/rc.d/ added.
hplip: No QT GUI.
wavpack: Newer version.
wpa_supplicant: No QT GUI.
xfce: Newer exo that fixes several problems.
xfce4-power-manager: Newer version.