It's really annoying when you can't see all of the SQL query window tabs you have more than 3-4 open (which is pretty much all of the time). It'd be nice to have them all on screen (a bit like Mozilla and Chrome tabbing) rather than having to select through each one to find the right window.
This is a handy piece of software: http://www.tabsstudio.com/download.html
Just a shame it's not free...