A common performance issue on web servers is cause by running out of physical RAM.
Rather than use top, run:
$ free -m
total used free shared buffers cached
Mem: 996 925 71 0 173 493
-/+ buffers/cache: 258 738
Swap: 2015 5 2010
Look at the -/+ buffers/cache free field - 738 in this example above. This shows the absolute amount of RAM left in megabytes. If that's looking low, say <5-10% of Mem total, you're running out of RAM.
If Swap used is more that 10% of Mem total, you might have already run out and paging to disk has started - this can be fatal for a web application.