Hey Jeff. mcEDU is defiantly the best way to go for a server. Like was mentioned before, mcedu makes it super easy to get server up and running already perfectly set up for the classroom.
I'm planning on using both mc and mcedu because one limitation of mcedu is it is only allowed to be installed on computers that are at the school. mcedu can not be installed on the students' home computers or laptops.
I'm working on making a normal mc bukkit server that students can join from home (or anywhere).
If you don't already know about mc plugins and servers, then setting up a normal bukkit mc server that functions similar to mcedu is A LOT of work and in the end is still not as easy to use as mcedu. You can have a mcedu server up and running in minutes, where as if you want to set the same thing up on a bukkit server, it will take a long time to get all the plugins configured and working properly, and you still don't have the functions and ease of use like mcedu. For a normal server there are literally 15k plugins to sort through and then you have to worry about compatibility and config of each plugin and you have to remember lots of commands (mcedu uses a very easy point and click teacher menu so you don't need to know commands or worry about permissions).
Also, the NPC plugins for bukkit are difficult to learn and not nearly as good as the NPC mod that comes with mcedu.
(worldedit is the exact same in both though)
It would be super awesome if mcedu's license allowed for students to install the software at home, but alas, I was informed there are no plans for this.
And just a side note for the mcedu dev team... a few bukkit plugin functions that would be cool additions to mcedu = dynmap, towny, and iconomy.