What should one do who used a free means of transportation belonging to a company where he previously worked, even though it is designated for current employees, and now feels a pang of conscience?

You must repent to Allah for using the transportation without payment or permission. Part of repentance is to render the rights to their rightful owners. The conditions for repenting from a sin related to the rights of a human being are: to cease the disobedience, to regret it, to resolve never to return to it, and to clear oneself of the right of its owner by returning the money or its equivalent. Therefore, you must calculate the number of times you rode the bus and pay the fare to the company, or seek forgiveness from the management. It is not a condition for rendering the right to inform them of what happened; rather, it suffices to deliver the right to the company by any indirect means, such as delivering it through a third party.