I’ve always found the man page for top to be painful to get through1, so I was quite happy when I found some old tips on how to get the most out of this nice utility. Not everything is in there, but it should be enough.
Another thing I’ve been looking for since ages ago is iotop (available in Debian and Ubuntu), letting you monitor disk activity on a per-process basis. This feature requires kernel version 2.6.20 or later.
1 In a way it feels like reading the man page for mplayer from end to end, albeit 7,000 lines shorter.
Update 7 April: thought I might as well mention jnettop too (its package name in Debian and Ubuntu), and you should of course know about dstat.