linux - How can I measure actual memory usage from my running processes?

I have two servers, server1 and server2. Both of them are identical HP blades, running the exact same OS (RHEL 5.5). Here's the output of free for both of them:

### server1:
             total       used       free     shared    buffers     cached
Mem:       8017848    2746596    5271252          0     212772    1768800
-/+ buffers/cache:     765024    7252824
Swap:     14188536          0   14188536

### server2:     

             total       used       free     shared    buffers     cached
Mem:       8017848    4494836    3523012          0     212724    3136568
-/+ buffers/cache:    1145544    6872304
Swap:     14188536          0   14188536

If I understand correctly, server2 is using significantly more memory for disk I/O caching, which still counts as memory used.

But both are running the same OS and if I remember correctly, I configured both with the same parameters when they were installed. I did a diff on /etc/sysctl.conf and they are identical.

The problem is, I am collecting memory usage and other metrics over a period of time, (eg: vmstat, iostat, etc.) while a load is generated on the system. The memory used for caching is throwing off my calculations on the results.

How can I measure actual memory usage from my running processes, rather than memory usage by the OS for caching? Is used - (buffers + cached) a valid way to measure this?