I have been running drush scripts (for Drupal) with Cygwin on my relatively fast windows machine, but I still have to wait about a minute for any drush command (spe
Also look at things that slow down Cygwin startup:
Trim down your Windows PATH (to the bare bones like %SystemRoot%\system32;%SystemRoot%)
Remove things you don't need from bashrc and bash_profile
Move things you only need in your terminal window from bashrc to bash_profile
One surprisingly large time suck in Cygwin is Bash completion. If you are using it (and you should because it's great), only source completion for the commands you need (rather than all of them which used to be the default). And, as mentioned above, source them from bash_profile, not bashrc.