The last several batches of beer I made had problems with carbonation after bottling, and the problem was eluding me.  I had a conversation with a fellow home brewer at work who helped me determine the cause: yeast dying before the bottling process was complete.

The problem started when my yeast starters were creating very active fermentation, reducing the fermentation time and increasing the alcohol content.  I also compounded the problem by waiting 1 or 2 days longer than I should have to bottle, after the fermentation was complete (i.e. over 1 minute between bubble bursts.

So in my last batch of beer (Stout), I tried something different: I saved some of the yeast I was pitching in a sanitized container, and stored it in my fridge.  As I was siphoning the wort into the bottling bucket, I added the stored yeast and the fermenting sugars to the wort.  It worked.  Only 5 days into conditioning, the bottles were producing the usual 1-2 inch head I expect.

Lesson learned: the very by-product produced by yeast (alcohol)  as it consumes its food (sugar) is toxic to the yeast itself.  So carefully watch for the time when the bubbling cycles go below 1 minute.  That means your yeast is gasping, and it needs new food to continue its life.