How can I figure out what's opening a Terminal window whenever I log in?
This might not be too helpful, but you can always check the date you downloaded things in your Applications folder and (if you remember the date, even vaguely) if you delete it, or anything non-essential near that date, then go by the process of re-installing what you want to find out what is causing the problem (or just leave them uninstalled). 

This is my recommendation, and if you are still seeing problems I would recommend Apple Tech Support (the official one).