Lots of detail has been stripped. Command is the main class, holding the lists. ModuleChoose is a sample usage.

Command.java

public abstract class Command implements Comparable<Command> {
    private static final Map<Command, Object> cmdSources = Collections.synchronizedMap(new HashMap<Command, Object>());
	private static final Map<String, Command> cmds = Collections.synchronizedSortedMap(new TreeMap<String, Command>());
	private static final List<String> aliases = Collections.synchronizedList(new ArrayList<String>());

	public static enum EType {
		Channel, Private, Notice, Console;
	}

	public static void addCommand(Object source, String name, Command command) {
		cmdSources.put(command, source);
		cmds.put(name,command);
		aliases.add(name);
	}
	public static void addCommands(Object source, Command... commands) {
		...
	}
	public static void addCommands(Object source, Map<String,Command> commands) {
		...
	}
	public static void removeCommands(String... commands) {
		for (int i = 0; i < commands.length; i++) {
			Command cmd = cmds.remove(commands[i]);
			if (cmd != null) {
				cmdSources.remove(cmd);
				aliases.remove(commands[i]);
			}
		}
	}
	public static void removeCommands(Command... commands) {
		...
	}
	public static Command getCommand(PircBotX bot, User sender, String channel, Command.EType type, CommandCallback callback, String message) {
		String[] args = message.split(" ");
		if (args.length==0 || args[0].length()==0)
			return null;
		String cmdName = args[0];
		Map<String,Command> matchMap = getCommands(cmdName, channel);
		if (matchMap.size()==1)
			return matchMap.values().iterator().next();
		else if (matchMap.size()>1)
		{
			String[] keys = matchMap.keySet().toArray(new String[0]);
			String s = String.format("Did you mean: %s or %s",StringTools.implode(keys, 0, keys.length-2, ", "), keys[keys.length-1]);
			callback.type = EType.Notice;
			callback.append(s);
		}
		return null;
	}
	public static boolean matches(Command command, PircBotX bot, EType type, String channel, String cmd) {
		if (type == EType.Channel) {
			if (cmd.length()<=1)
				return false;
			if (!Data.forChannel(channel).getString("main-cmdchar").contains(cmd.substring(0, 1)))
				return false;
			cmd=cmd.substring(1);
		}
		return getCommands(cmd, channel).keySet().size()==1;
	}

	public final int compareTo(Command command) {
		return command().compareTo(command.command());
	}

	public abstract String command();
	public abstract String help(PircBotX bot, EType type, Channel channel, User sender);
	public void visible(PircBotX bot, EType type, Channel channel, User sender) {}
	public abstract void doCommand(PircBotX bot, EType type, CommandCallback callback, Channel channel, User sender, String message);

	public String toString() {
		return command();
	}
}

ModuleChoose.java

public class ModuleChoose extends Module {
    public void onEnable() {
        Command.addCommands(this, cmd = new CmdChoose());
    }
	public class CmdChoose extends Command {
		public String command() {return "choose";}
		public String help(PircBotX bot, EType type, Channel channel, User sender) {
			return "choose {1} {2} ... {n} - makes a decision";
		}

		public void doCommand(PircBotX bot, EType type, CommandCallback callback, Channel channel, User sender, String message) {
            if (Data.isBlacklisted(event.getUser())) return;
			String[] args = message.split(" ");
			if (args.length == 1) {
				callback.type = EType.Notice;
				callback.append(help(bot,type,channel,sender));
				return;
			}
            ......
		}
	}
}