Hufflepuff won the Quidditch Cup that year. Giving Harry, Fred, George, Ron and Hermione points for the Sirius Black debacle would've required that Dumbledore justify those points, as he was not one to abuse the point system, so he decided not to. None of them truly cared about House Points anyway, being busier with other things.
Ravenclaw had hit Rock Bottom on the matter of points after Flitwick was done with the female half of his house. On the flipside, Luna Lovegood was a very happy girl indeed, since nobody had the balls necessary to tackle on the Potter family.
Slytherin got in third, mostly due to Snape doing his hardest to keep Slytherin's point count afloat. Most of the snakes had earned themselves no sympathy whatsoever from the teachers other than Snape, with their antics. Turns out most teachers being Light Aligned and most Slytherins being the sons or daughters of Death Eaters makes for a biased point system. That the children were following in their parents' footsteps wasn't helping.
Gryffindor enjoyed no outrageous point losses, well other than Neville Longbottom's losses during potions class, or wins, so they hit a comfortable, if distant, second place.
Hufflepuff's team spirit helped pull them through, having a positive effect against the dementor-induced depression that had afflicted everyone else's grades, attitudes and temperaments. The house partied like it was 999, since it might as well have been that long since they'd won the House Cup.