For sims 3, besides meticulously checking file after file is there an easier way to check for duplicate CC? A program that does it at the click of a few buttons maybe?

There is Sims 3 Dashboard. it's not the most accurate (as there are mods who actually look like they conflict/duplicate of each other but they are not). But that should be the only way. But your CC have to be installed via .package.

At the risk of sounding redundant: When it comes to packages: Windows explorer, click on file name to sort them alphabetically.
Sims3 packs: CC Magic . It has a search function. Works for packages too if you install them with it.
Tutorial on how to use it: https://nonasims.wordpress.com/?s=CC+Magic

I use the Dashboard, as well. It's so simple and quick to use. When it comes to conflicts (shown in the list in dark orange color) it's good to remember that as long as those conflicting files are by the same creator, it's perfectly normal. If the files conflicting each other are by different creators, then you have a problem. Duplicate files are shown in the dashboard list in bright yellow, so they are easy to spot.

http://modthesims.info/d/387006

Just to expand for more detail on the Dashboard varpunen linked to. See Understanding Mods and CC Conflicts with Delphy's Dashboard. When the Simlogical site went down the mods & details were moved to a different area and this one is incomplete and lacks the format and detail of the original so make sure to click on the link next to "***Read the whole of this Tutorial in..." for the original illustrated Tutorial by Nona Mena in PDF format.

I'm trying to organize my Sims3Pack downloads backup folder to get rid of all duplicates I may have in it. What program does this?