In essence, that's the percentage of guilds raiding who've completed that achievement. And the toughest achievement in the game right now is The Immortal, which requires you to get 25 people through Naxx without dying once. Only about 1.5% of guilds raiding have finished that one. After that, it's Heroic: You Don't Have an Eternity (take out Malygos in six minutes), and Heroic: Shocking! (bring down Thaddius without crossing charges). The hardest 10-man achievement is the non-Heroic version of the Malygos timed achievement -- The Undying actually isn't too bad, with almost 20% of guilds having attained it.
More after the break, including information on the easiest raiding achievements.
On the other end of the scale, the easiest achievements are the zero-drake Sarth kills, and the Naxx wings achievements: most guilds seem to beat them in the order of Arachnid, Plague, Military, and Construct if this data is comparable to all of the game's guilds. In general, 10-man achievements are easier than 25-man ones (since coordinating more people is usually harder), but that's not always true: the 25-man Sarth 3D kill has a higher achievement rate (about 16%) than the 10-man version (around 7%), and in fact, the 2D 10-man is close to the same rate as the 3D 25-man, putting them at about the same challenge.
Like I said, fascinating stuff. Note that this is a self-selected sample, so while it may represent a good portion of the game, it doesn't represent everyone (PuGs wouldn't be included in these stats, nor would any guilds who haven't registered in Guildox). But it makes a lot of sense, both in terms of how players have perceived the fights already and in terms of which fights are presumed to be progression fights. It would be interesting to see achievement information like this from Blizzard at large -- these are just raiding achievements, but what would be the most difficult achievement across the board? We'd like to hear from Blizzard what kind of achievements are most and least completed on an Azeroth-wide scale.