As an essential step towards the Minecraft modding API, and also for sanity's sake in our own code, we're removing Texture Packs and replacing them with a new Resource Pack system. Ultimately, every mod/plugin will be its own resource pack, vanilla will be a resource pack by itself, and users will be able to apply multiple resource packs at once.
Resource packs will be able to change any type of resource, from sounds to fonts, and not just textures. We're also including a new metadata format so that we (and mods/plugins) can easily include whole new types of resources with very minimal difficulty. Unfortunately, this means that all current texture packs will break... We'll be working on another unstitcher-like tool to aid with the conversion, and hopefully this will be the last major breakage to texture/resource packs in the foreseeable future. The new format will allow us to more easily detect out of date packs and possibly even load them as if they were up to date.