RE: Minecraft
I think after 1.3 they are finally going to work on the Modding API. They did the whole SP and MP merge in 1.3 to make everything compatible. I'm excited, but I think it's going to be a nightmare for server admins/mod devs. The Bukkit team is now working for Mojang in creating an official server software like Bukkit. However, this means that Bukkit is going to die soon, and with it, all the plugins. (This has pretty much been confirmed) All the public severs now will have to wait in 1.3 until plugins get completely re-written (which will take a long time, if the plugin devs even decide to do it, or it's even possible/practical with the new official software), or move to Spout. Spout used to be a plugin for Bukkit (and still is I guess...) that gives the server moddability. This means that you can have custom blocks, items, mobs, etc as long as each player has the Spout Mod installed. Recently, Spout has written it's own server application to mimic Bukkit, and are also writing a plugin for it called BukkitBridge. This will allow Spout to use old Bukkit plugins. This is good news for anyone who wants to keep with the old experience and not re-build servers and config files entirely.
However. I believe that the official server software that Bukkit and Mojang are building will allow the server to be modded (with the new Modding API, no less) and have the mods automatically installed onto any client that connects. (Probably with permission, of course) I think there was an IRC discussion about the Modding API the past week or so, and this was discussed. It's totally possible now that SP and MP are the same thing.
If this does become a reality (I really think it will in the future) it would totally revolutionize the way people play on MP servers. Can you imagine the possibilities?