Copy&Paste is bad.

Essentials/src/com/earth2me/essentials/Essentials.java

@@ -96,6 +96,10 @@ public class Essentials extends JavaPlugin implements IEssentials
 
 	public void onEnable()
 	{
+		if (!Thread.currentThread().getStackTrace()[5].getMethodName().equals("loadPlugin")) {
+			logger.log(Level.SEVERE, "Another plugin is trying to enable Essentials manually. Don't do this! It's probably "
+					+ Thread.currentThread().getStackTrace()[5].getClassName());
+		}
 		if (enableErrorLogging)
 		{
 			logger.addHandler(errorHandler);

Essentials/src/com/earth2me/essentials/register/payment/Methods.java

@@ -68,14 +68,6 @@ public class Methods {
             if(method.getDescription().getName().equals(name)) plugin = method; else  plugin = manager.getPlugin(name);
             if(plugin == null) continue;
 
-            if(!plugin.isEnabled()) {
-                this.self = true;
-				Logger.getLogger("Minecraft").log(Level.SEVERE, name + " Plugin was found, but not enabled before Essentials. Read the Essentials thread for help."); 
-                //manager.enablePlugin(plugin);
-            }
-
-            if(plugin == null) continue;
-
             Method current = this.createMethod(plugin);
             if(current == null) continue;
 
@@ -99,9 +91,7 @@ public class Methods {
                             break;
                         }
 
-                        if(this.preferred.isEmpty()) this.Method = attached;
-
-                        if(count == 0) {
+                        if(count != 0) {
                             if(this.preferred.equalsIgnoreCase(attached.getName()))
                                 this.Method = attached;
                         } else {

EssentialsGroupBridge/src/com/nijikokun/bukkit/Permissions/Permissions.java

@@ -3,6 +3,7 @@ package com.nijikokun.bukkit.Permissions;
 import com.nijiko.Misc;
 import com.nijiko.configuration.DefaultConfiguration;
 import com.nijiko.permissions.PermissionHandler;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.anjocaido.groupmanager.GroupManager;
 import org.anjocaido.groupmanager.permissions.NijikoPermissionsProxy;
@@ -55,6 +56,10 @@ public class Permissions extends JavaPlugin {
 
     @Override
     public void onEnable() {
+		if (!Thread.currentThread().getStackTrace()[5].getMethodName().equals("loadPlugin")) {
+			Logger.getLogger("Minecraft").log(Level.SEVERE, "Another plugin is trying to enable Permissions manually. Don't do this! It's probably "
+					+ Thread.currentThread().getStackTrace()[5].getClassName());
+		}
         Server = this.getServer();
         PluginDescriptionFile pdfFile = this.getDescription();
 

EssentialsGroupManager/src/org/anjocaido/groupmanager/GroupManager.java

@@ -63,6 +63,10 @@ public class GroupManager extends JavaPlugin {
 
     @Override
     public void onEnable() {
+		if (!Thread.currentThread().getStackTrace()[5].getMethodName().equals("loadPlugin")) {
+			logger.log(Level.SEVERE, "Another plugin is trying to enable GroupManager manually. Don't do this! It's probably "
+					+ Thread.currentThread().getStackTrace()[5].getClassName());
+		}
         GroupManager.logger.setUseParentHandlers(false);
         GMLoggerHandler ch = new GMLoggerHandler();
         GroupManager.logger.addHandler(ch);