Google Reader
I’ve been trying out Google Reader for a few months, and found the lack of subscription-time feed organization to be a real pain.
But they've completely fixed this with their most recent update:
In addition to the subscription-time feed organization issue, I've also found it frustrating that I couldn't move a feed to another folder while reading it. They've also fixed this:
Google Reader and the Reader team get major, major points from me for this!