Accounting for every byte of memory used in a virtual memory system is just not possible. However, you can find a fairly accurate figure for the total amount of free memory, excluding that taken by buffers and cache, using the free command. By monitoring it over a period of time and with different workloads, you should become confident that it will remain within a given limit.
When you want to tune memory usage or identify sources of unexpected allocations, there are resources that give more detailed information. For kernel space, the most useful information is in /proc: meminfo, slabinfo, and vmallocinfo.
When it comes to getting accurate measurements for user space, the best metric is Pss, as shown by smem and other tools. For memory debugging, you can get help from simple tracers such as mtrace, or you have the heavyweight option of the Valgrind memcheck tool.
If you...