I am far from an expert so take this with a grain of salt...
Before you do *anything* (and I'm certainly not recommending you actually do anything), backup the folders you are going to toy with.
Step 1: would be to check the size of each folder. If they are small, you are likely better off just leaving them be.
Step 2: is to not touch anything in /var. I don't know what all the directories are, but I recognize MobileDevice and db as being things your probably don't want to touch.
Step 3: from my limited understanding of things, you should be okay to remove some of the duplicate directories in the /Library directory. I wouldn't touch MobileDevice, Keychains or db though.
Like I said, unless these directories are taking up a lot of room, you are almost certainly better off to leave them be. I don't know why you have these duplicate directories, but it may be related to apps you have installed that I do not.