When installing some apps, I get an "Extras" folder, where do I put this? I'm new to Macs. I understand how to install Apps by dragging and dropping into the Applications folder and then opening the App, but sometimes installations come with an "Extras" folder (for instance, Diff Merge - http://www.sourcegear.com/diffmerge/).

Is there a common place to put things like this, or are these just tools I need to copy to various locations like my PATH?
An "Extras" folder inside a DMG file has no particular significance, it is just a subfolder distributed with the disk image and could just as well go by any other name. Therefor there is no generic answer to your question.

In the case of your example DiffMerge, the "Extras" folder contains a Readme.txt with suggested instructions on how to install these additional utilities.

 sudo cp Extras/diffmerge.sh /usr/bin/diffmerge
 sudo chmod 755 /usr/bin/diffmerge
 sudo cp Extras/diffmerge.1 /usr/share/man/man1/diffmerge.1
 sudo chmod 644 /usr/share/man/man1/diffmerge.1