Save screenshot with custom name
Changing the prefix part of the names

defaults write com.apple.screencapture name "My Screenshot"
killall SystemUIServer


Changing the format of the names

f=/System/Library/CoreServices/SystemUIServer.app/Contents/Resources/English.lproj/ScreenCapture.strings
f2=~/Desktop/ScreenCapture.strings
sudo cp $f $f2
sudo chown $USER $f2
plutil -convert xml1 $f2
open $f2 -a TextEdit


Change

&lt;key&gt;%@ %@ at %@&lt;/key&gt;
&lt;string&gt;%@ %@ at %@&lt;/string&gt;


To something like

&lt;key&gt;%@ %@ at %@&lt;/key&gt;
&lt;string&gt;My %@ %@ at %@&lt;/string&gt;


(The default format is currently something like Screen Shot 2012-06-12 at 8.02.40 AM depending on the locale settings.)

sudo chown root $f2
sudo cp $f2 $f
killall SystemUIServer


Changing the default location

defaults write com.apple.screencapture location ~/Pictures/
killall SystemUIServer


Using custom scripts

I've disabled the default shortcuts and have assigned shortcuts to scripts like screencapture -i ~/Desktop/`date '+%y%m%d%H%M%S'`.png.