We're essentially a large consultancy who bills by the kousuu -- "unit of engineering labor", somewhat arbitrarily defined as "what we think one engineer should be able to do in a day". Projects are successful if we bill more than N * K * the average labor cost of producing one kousuu, where K is the number of kousuu and N is a constant representing overhead, profit, and the cost of sale.
Projects are sized based on a negotiation between us and the customer. It is then broken into parts, which are given their own kousuu value, via guesstimation by a senior engineer on the team. (You'll notice this process involves an awful lot of guesstimation. This tends to converge on reasonable numbers because guesstimation is happening among multiple actors who don't have an incentive to collude -- kinda-sorta like a market of players with imperfect knowledge can converge staggeringly quickly on a good guess of the intrinsic value of something.)
We then measure how many kousuu of work you complete for a particular project per day you report you are working on the project. That is currently our primary productivity measure, although we also track customer satisfaction, "claims" (a backchannel by which customers here get free work done to fix issues in the deliverable which are determined to be due to our mistakes), subjective quality assessments from the engineers, follow-on business from the same customer, and any value we can extract from the project for the company. (For example, in a 10 kousuu project if we manage to extract 2 kousuu worth of functionality that the customer paid for into our internal framework, then deploy that to seven customers and charge them each for it, we make out like bandits.)
Anyhow, we keep obsessive records of who does what and how long it took, so figuring out productivity is "just" a matter of dividing. (We only figured out the dividing trick recently. Hard to move a large organization from the way it typically does things, you know?)