Where is the rest of the memory??? and why is it so much lost to "programs"???
Hard Drives are not referred to as memory. They use the same terminology for measurement but memory and storage are used differently and are technologically distinct. RAM is memory (SDRAM, DDR, DDR2 and RDRam are several forms or memory).
Each hard drive is formatted in clusters (typically 4k or 4096bytes.) each program stored on the drive uses 1 or more clusters. On average 1/2 of one cluster (the last one) used by each program is lost (2k or 2048 bytes). With a large number of files (and directories which also use HD capacity) you can lose a significant amout of usable space. One of my partitions holds 18522 files which results in (on average) a loss of 18522x2048 bytes or 37,933,056 bytes (~36.2 megabytes) out of almost 78 gigabytes in files.
This is rather like in some books (mostly manuals) a page will be blank between chapters with the note "This page intentially left blank" as they use the concept that both sides of a page are used in the same chapter or left blank. The 1/2 cluster per file is like that blank page.