One factor to "file size says X but more-than-X disk space is missing" is that disk space is allocated in blocks, so any unused space on a block that's been allocated for a file is unusable, but not counted in the size that's listed for the file. On a huge file, it's trivial, but if you have a ton of small files it's pretty significant. On Windows I think the default is 4096 bytes. So in an extreme case, if you had 100,000 1 byte files looking at the file sizes you'd think you only used 100,000 bytes, but really you just lost 400 megabytes of usable disk space...
One thing I periodically do is search for big files - use the windows search, put a big number in the "search options -> size" like 50000 Kbytes, will find all files 50,000,000 bytes or larger, then see what the heck those are - is it something I downloaded and forgot about, is it some huge error log something is creating, whatever.
Other things to check - empty the recycle bin, clean out your TEMP directory, check what files your antivirus program might have put in quarantine. At various times each of those things used up a scary amount of my disk space. Oh, and Chrome, which not only loves to use up all my RAM but it likes to keep a copy of every update it ever made - I had well over 1G of those at one time too.