Long delay after issuing commands at prompt

This has only begun recently, so I assume I've done something wrong but I havn't tinkered that much, so I can't really retrace my steps.
At the prompt when I type in certain commands there is a very long delay (10-30 seconds) to load certain things. startx is one of them, emacs and firefox are others.
There isn't really anything else to say, there isn't any error messages or anything so I really have no idea how to locate the problem. It also occurs outside of a prompt, for instance when using xbindkeys.
After they've been loaded once they load quickly but it's really annoying after I reboot.
Any clues?

I find that there is a small delay normally with those programs, I'm not sure if that's what you mean.
Could you post the contents of /var/log/errors.log and the output of dmesg.  Also you might check the CPU
usage when they open.

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