Ok, So I'm planning to format my desktop pc and reinstall my windows operating system. Fresh install. I got about 100 installed steam games, you know, in the computah. My problems is I have saves that I don't wanna lose, skyrim for one. Now I figure some games use cloud saving but not every game. My question is, are my saves for every game all in the Steam>steamapps>common folder?

Ya, all the games files are in those folders. Pretty sure the saves are as well.  
Some may be in your %appdata% as well (if you have windows 7 just do a search in the start menu search bar for %appdata% and hit enter- look for the folders for certain games there).

Not all of them. Some are in the Steamapps folder, some are in My Games, some are in Saved games. I suggesting looking in all of those places and copying them all to an external drive.

There are saves in the userdata folder in the steam directory as well. Those are encrypted and obfuscated for a reason. They protect the integrity of achievements. So, you wont know what they go to unless you do some detective work.

Searching the Steam Forums is what I always do to find my saves. I know some people also use Game Save Manager so I think that can be the easiest way to transfer saves but I have not personally used it. Supported Games.

http://www.gamesave-manager.com/

http://pcgamingwiki.com/wiki/Save_Game_Cloud_Syncing

Thanks for the answers guys! I had a feeling I was gonna have to do some detective work tracking down all my saves.

Well I found my game saves, they were in my other set of My Saves files. But this did help me find some adware ive been hunting for ages...kudos braaaa