Every time I restart my OS X Mountain Lion (10.9) laptop, it stops using the DNS search domains I've added via the Network preferences pane. I have found that restarting mDNSResponder fixes this issue. There are two ways to do this.

The first is a simple restart by sending a SIGHUP to the process:

sudo killall -HUP mDNSResponder

The other option is to stop and start the process with the launchctl command:

sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.mDNSResponder.plist
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.mDNSResponder.plist