Is there an analytical chemistry alternative to the Scoville scale for the hotness of chilli?
Matt did find a method that uses HPLC on the peppers alone, not in a dish. 

So given that the capsaicinoids is a class of compounds, each different capsaicinoid would have a different perceived hotness. So a chemical test would measure the concentration of each type capsaicinoid and then use a weighted average over the human perceived hotness for each member of the capsaicinoid class.