Question: I have a selection of paths in illustrator (cs6).

I want to select all the paths and free transform them to something like a 3rd of the size. The problem is when I shrink them down, the stroke on the paths stays the same. So originally some had 1pt and 2pt stroke, bit when I free transform all the paths to a 3rd of the original size, the strokes are all still 1pt and 2pt big.

I don't want to have to go through each path and change the stroke, as it would take a long time. is there a tool/option in illustrator that can help with this?

Answer: 
Using the Scale tool, tick the check box which says "Scale strokes and effects" before scaling. That reduces your strokes proportionally.
I find using the keyboard "CMD-K" or "Ctrl-K" and selecting/deselecting the scale stroke and effects option is the easiest and fastest route to keep control of an scaled object's appearance.

You can also turn the object/s into a symbol and then you can scale to your heart's content and when you need to edit the paths again they won't have a bizarre pixel size, like 3.544px instead of 1px. Symbols are terrific for keeping absolute control of accurate work.