Form letters are the worst. They mean one of two things. 1) the publisher was to busy (to many submissions) to respond individually or 2) your submission didn't merit anything more than a formulated response. Either way, no rejection feels as empty as a form letter.
But a more personalized rejection can sometimes leave you scratching your head. I got one a few years back from a leading (pro-rate) online horror zine, that said they were rejecting my submission because it was to much like what they publish.
Anyway - I got two rejections this week, the first was a form rejection for a short story for Comet Press's new horror anthology. But the second was from Fantasy Magazine, and Fiction Editor Cat Rambo wrote some encouraging words, saying my submission came very close and I should definitely try them again. A rejection letter like that will probably keep me going for the next six month.