How do I fill up a massive hole in the world?

Solution 1:

At the moment there are chunks that are filled with air.

If you go into MCEdit (for example) you can remove the offending chunks and then when you reload the world they will regenerate.

In MCEdit use the selection tool to highlight the offending chunks then click "Select Chunks" followed by "Chunk Control". Then use the "Delete" option. Save and quit.

You can tell if the chunks are still there as there will be a checkerboard "background" in MCEdit. If the chunk is missing completely the background will be blue.

As MBreadley points out you should take the Minecraft server offline before using another program to edit the world.

Solution 2:

If you're using Bukkit it's as simple as using this regen chunks mod. It allows you to just /regen the chunk you're in. Use with care!