I'd like to see more software nudge people in the direction of GTD's low-stress productivity.
World of Warcraft organizes your quests according to where you discovered them, not according to where you can make progress on them. You can easily have your character in the right town but forget to advance one of your quests.
Since the game's quest organization is so unwieldy, it limits players to 25 quests. This forces some players to abandon quests with the intent of picking them up again later. But more importantly, "only write down the most important stuff" is the wrong message to send to our children.
Having to maintain your own lists outside of the game makes playing the game too much like work. If instead, the game subtly taught players how to work effectively, they might have more time to play.
Thunderbird's default set of color labels reflects priorities and reasons (important, work, personal, to do, later). These labels don't really help move messages out of the inbox.
Instead, Thunderbird should suggest contexts and non-action sets (home, office, errands, waiting for reply, reference).
Firefox has the distinction of containing three dangerous stuff magnets: the bookmarks menu, the bookmarks toolbar, and session restore. I've seen several coworkers fall into the session restore trap, and it's not pretty: with hundreds of tabs, Firefox can take minutes to start.
I like Jono's suggestion of replacing bookmarks with features that speak more directly to use cases like to-read, sharing, and reference. Firefox 3's tags make reference possible but not much else.
To-read is the trickiest, since it can't really be organized. Separating to-read from sharing and reference is enough to keep those other categories clean, but to-read has to work if it's going to be used. Maybe Firefox can include hints about how to use to-read effectively, like having an "airplane" button you click to open all of them in tabs just before you disconnect from the tubes. Or maybe Firefox can keep those items ready for reading without the overhead of having them open in tabs all the time.
What other software could encourage people to discover contexts and the next-action principle? Where else can workflows be improved, so collection buckets are emptied naturally, and users don't need to make a special effort to "stay organized"?