Loo writes on the official forms that the team will basically redesign the game's API, which means unofficial developers everywhere will be able to hook into the game's mechanics much more easily and smoothly. Mojang points out that there are a few teams that have made popular mods for the game, including Spout and Forge, but the Bukkit team was chosen because they've developed specifically for Minecraft servers. The plan is to have them working on "more than just modding."
Obviously, the gentlemen are quite excited about joining the Mojang guys. That tends to happen when a company whose game you work on for free decides to start paying you in real money.