At Confoo I had an interesting conversation with Guilherme Blanco regarding the fact that in Doctrine 2 they had a performance issue due to usage of array_key_exists() and how it was significantly slower than isset(). His anecdotal example was that doing isset() took 0.5 seconds, while array_key_exists() for the same operation took 5 seconds! That seemed wrong [...] so, I've decided to do a quick benchmark using a 5,000 element array.
His benchmarking code is included - it just loads up a simple data set from a file of "words" and measures the microtime between the isset and array_key_exists calls. His results do show that isset is the faster of the two (by 2.5x) but it's still a super small micro-optimization that won't gain you much in the end.
The bottom line is that if your application does not need to distinguish between an array key that does not exist and one whose value happens to be NULL you should use isset() because it happens to be a little faster.