I've found that one thing that was very helpful for me was to keep history per machine. For me having the history make sense in the context of the system function is very valuable and I know that I won't get other commands that I don't need or want to see in my history.

What I do it HISTFILE=$HOME/.history/`hostname`.history so then I have a nice record of what I've done on all the machines I log into. This is particularly nice when you have a central home directory.