Quick and dirty: Why don't the memory usages reported for each program from 'ps -aux' and/or 'top' (even after pressing the "H") add up to the totals as being reported by 'top' and/or 'free'? Try it and you'll see what I mean.
Variety of reasons:
Some processes share memory. Different instances of the same program will share code pages. Different programs entirely will share code pages when they use the same libraries. Multi-threaded programs will share both code and data pages. This sharing makes the sum of the memory sizes too big.
The X server will mmap your video card's memory, so its size appears considerably bigger than it really is.
You may also be looking at the wrong piece of output from 'free' or 'top', entirely. The "total" memory use reported by 'free' includes application memory use as well as disk buffers and cache.
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