I've been playing Fallout 3 GOTY on steam for the past few weeks, recently i was in my documents and decided to put all of the game saves into one folder to neaten things up. Now when i start up Fallout 3, i don't get the option to continue from where i left off, even after un-doing what i did before. Any hope or am i screwed?

1 neat folder for saves is only when you use GFWL exclusively or offline exclusively. They each require their own folder.
Plus if you messed up the path to it. From Mydocuments , it goes Mygames\Fallout3\saves , by just creating your own path , that would explain why you dont see them. Each desktop user will have their own path also.

To fix the path ... just delete the fallout3 folder found in "Mygames" After putting your saves outside it (maybe you allready did?"
Then restart the game past the introduction. close the game.
Then copy paste your saves back into the save folder found inside Mygames\fallout3
For GFWL , there is a folder inside saves with your logon name.
You can freely copy paste .fos files between these 2 , but you have to have each one to access saves from the different game instances. Same goes for different desktop user accounts.