Workbench isn't really designed for doing cross-org operations without logging out and logging back in. If they are just queries, you could use the saved queries feature to use the same queries between multiple org. To do this, first go to Settings | Persist Saved Queries and Searches | All Organizations | Apply Settings, and then go to SOQL Queries and when you save a query it will be available to you (and only you) when you log into other orgs. This is still a pretty manual process if this is something you'll be doing a lot. If its something you'd like to automate and you are comfortable with coding, it would probably be easier to just write an API script that logs into multiple orgs, runs queries, and aggregates results. Depending on how complex you want to make this and if you need data to be presented to end users, you might even consider creating an app on
Heroku that does this on the backend and then presents it to users in
Force.com Canvas.