I figured I'll release most of the MC Server source here. All of it will probably be here in time! It's work in progress and this is for the 1.4_01 server, I'm sure you can figure out how to apply it to 1.5_02+ if you really wanted to though. This isn't a very complicated mod, it contains minor modifications to op commands, new recipes (Which I'll outline minorly), apple modifications (for rp purposes, will be explained later), and new login / logout messages.

First I'll outline op commands, the changes are as follows: It's pretty easy to rename commands and remove them from /help so I'm not going to be outlining that. The file I modified was "ConsoleCommandHandler.java".

Here is my /say modification:
serverconfigurationmanager.sendPacketToAllPlayers(new Packet3Chat((new StringBuilder()).append("\247d[").append(s1).append("] ").append(s).toString()));
That's line 3 in the /say if statement. It's a pretty simple motification to display the username of the op, "append(s1)" is the command user's username.

Here is my /list modification:
String players = serverconfigurationmanager.getPlayerList().toString();
Integer pCount = players.split(", ").length;
icommandlistener.log((new StringBuilder()).append("Connected players: (").append(Integer.toString(pCount)).append(") ").append(players).toString());
Here, I store the list of players to "players", I then store the amount of players to "pCount" by splitting it into an array and returning the length, then I piece it together using a StringBuilder. Another simple modification.

Next, I'll outline the apple modifications. The changes are as follows:

The files I edited were "Item.java" and "ItemFood.java". I only had one change in "Item.java" and that was I changed the amount of health it heals to "-1" meaning when eaten, it will deal .5 damage to the player. My "ItemFood.java" modification makes apples (red and golden) stackable, which is within the "ItemFood" method on the last line:
if (i == 4 || i == 66) maxStackSize = 64;
else maxStackSize = 1;
I'm sure there's a better way of doing this though as cookies are stackable to 8, when I wrote that there were no stackable foods though. I'll update this later.

I won't be outlining all my custom recipes as most of them haven't been discovered yet but some back been here: http://minecraft.pho3n1x.com/forum/index.php?board=6.0. I simply edited "RecipesCrafting.java" and added in my own recipes. I won't be outlining how to do that though as it's widely considered one of the easiest modifications to do and I'm sure with a little research you could figure it out yourself.

Thanks for reading! I hope this helps out someone else creating an RP server or doing minor server modifications.