OS X will account for most of those files. Applications you download are usually packages that could contain thousands of files for a single application. My system has well over one million files, and they take up lots of space on backup drives.
Apparently, you don't have permanent backups. You may want to consider the importance of having such backups so you don't have to keep data you don't use often stored on your startup drive. Or alternatively get a larger hard drive.
Time Capsule backups are no truly permanent because over time old files no longer on the computer are pared out of the backup to make space for added backup files. In addition to the Time Capsule you might keep a separate storage drive to which you would transfer files you wish to retain but that are not likely to be used.
Then also consider maintaining a bootable clone of your system as a third backup that can be used in an emergency or if the main startup volume fails or becomes corrupted. See:
Get an external drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Although you can buy a complete external drive system, you can also put one together if you are so inclined. It's relatively easy and only requires a Phillips head screwdriver (typically.) You can purchase hard drives separately. This gives you an opportunity to shop for the best prices on a hard drive of your choice. Reliable brands include Seagate, Hitachi, Western Digital, Toshiba, and Fujitsu. You can find reviews and benchmarks on many drives at Storage Review.
Enclosures for FireWire and USB are readily available. You can find only FireWire enclosures, only USB enclosures, and enclosures that feature multiple ports. I would stress getting enclosures that use the Oxford chipsets especially for Firewire drives (911, 921, 922, for example.) You can find enclosures at places such as;
All you need do is remove a case cover, mount the hard drive in the enclosure and connect the cables, then re-attach the case cover. Usually the only tool required is a small or medium Phillips screwdriver.