Mysterious bash instances using a lot of CPU, how can I debug?

Take a look at the output of lsof | grep 'bash.*cwd'. That will tell you the current working directories of the processes.

If you have pstree, take a look at its output. If not, take a look at the output of ps aux -H. That will tell you which processes own these mystery processes.

Start looking through configuration files for anything suspicious. Here's an incomplete list of ones you should check:

~/.bash*
~/.profile
/etc/profile
/etc/bash*
/etc/cron.*/*

The [process name] means that ps can't find that process' arguments, including argument 0 which contains the name of the file that was executed to create the process. That means lsof /bin/bash won't find these processes.

You can also take a look at output of:

ps -p <pid> -o pid,user,tty,comm,args

Some shell scripts will appear as /bin/bash or perl in the output of top but args argument in the output of ps should give you the exact script running.