If you are looking for adding multiple junction objects at a time, the only solution is a custom Visualforce page.
For a slightly different problem, where we need to assign many of object B to object A, We have trained our users to do this with a view on object B. We are assigning Billing Accounts (B) to Payment Offices (A). The view on Billing Account has check boxes on the left side. The user checks the Billing Accounts to be assigned, then double-clicks on the Payment Office field on any of the checked rows. A pop-up asks if you want to update only the single row or all checked rows. By selecting 'all checked rows', the update is done to all of them.
The view is created by the user, who enters the selection criteria (name, address, state, etc.). All user-created views are visible only to them.