1. Port Forward. Do not pass go until you've finished this step.
2. Get the most recent Reccomended Build Bukkit.
3. Get the minecraft_server.jar that that is compatible with.
4. Open Notepad++ (or other non-Word text editor), and paste this (if you have Windows 7 64-bit):
@ECHO OFF
SET BINDIR=%~dp0
CD /D "%BINDIR%"
"%ProgramFiles(x86)%\Java\jre6\bin\java.exe" -Xincgc -Xmx1G -jar craftbukkit-1.0.0-SNAPSHOT.jar (change this part if your bukkit file is not named that, or change your bukkit file to match this name. whichever one works Don't copy this parenthesis part.)
PAUSE
Save as .bat file. (craftbukkit_starter.bat is a good obvious name, but whatever floats your boat.)
5. Place .bat file in same directory as minecraft_server.jar and the craftbukkit file.
6. Edit server.properties like a normal minecraft server. (spawn mobs on/off, world name, port, internal ip, etc)
7. Make a plugins folder inside your server folder. Place the bukkit mod files in there. (Permissions.jar, WorldEdit.jar, towny.jar, etc.)
8. Run server, then stop. Observe how bukkit has seperated the three default worlds into three folders. (world, world_nether, world_the_end. Name will vary if you aren't using default name.) Go back to plugins folder and configure any newly created configuration files in the mod folders you need to.
8a. Set up permissions here, if you're using it. Otherwise you'll have a lack of working commands. PEX is a good choice if you are.
9. Run server for real, if it worked in the previous step.
10. Do something! Or get more mods, either/or.