>    often taking 10 seconds to list just 5 files in an NFS-mounted

That  screams network issue. 

 + Check your network interface stats for errors  (ifconfig)
 + Check your duplex setting -- many switches do not really do "auto" well. 
Hard-coding to full-duplex helps, but if you have a managed switch, you need to 
make sure the switch ports are set to FD as well.
 + Swap network cables (I know, I know.. but its happened) 
 + Are you using any centralized user id store for user accounts? A long 'ls' 
could also be a slow libnss query trying to resolve uid -> user name 
 + syslog and 'dmesg' for kernel errors, as Johan mentioned

The error occurring with local disk is puzzling-- are you using any VM 
technology?

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