A decent portion of this space is taken up by Dalvik Cache. When you uninstall programs, the old dalvik cache associated with the uninstalled app usually gets left behind on the system, especially if you are rooted and have deleted a bunch of the built-in system apps.
If you're rooted, you can clean it up by using a root browser and going to the directory: \data\dalvik-cache\arm\ and selectively deleting stuff that you know is no longer installed on your system. Be aware that the names of these files may not associate directly with the name of the app as you refer to it. You need to find the name of the apk file or how the system refers to it and delete the .dex and the .art file associated with that app. After you delete what you want gone, reboot.
You could also just delete everything in that folder and the stuff that is still used/present on your device will get recreated when you reboot the phone. You will see the "Optimizing x apps" message after the boot process begins and it will be generating new cache files for those apps. If you delete all of them, this could take anywhere from 5 to 20 minutes depending on how much is on your phone and how fast the device is in general.