Adding the option to suppress overload warnings as a bukkit.yml option. Thanks oloflarsson for the PR.

src/main/java/net/minecraft/server/MinecraftServer.java

@@ -412,6 +412,7 @@ public class MinecraftServer implements Runnable, ICommandListener, IMinecraftSe
                     long l = k - i;
 
                     if (l > 2000L) {
+                        if (this.server.getWarnOnOverload()) // CraftBukkit - Adding an option to suppress these warning messages
                         log.warning("Can\'t keep up! Did the system time change, or is the server overloaded?");
                         l = 2000L;
                     }

src/main/java/org/bukkit/craftbukkit/CraftServer.java

@@ -321,6 +321,10 @@ public final class CraftServer implements Server {
         return this.getConfigBoolean("allow-nether", true);
     }
 
+    public boolean getWarnOnOverload() {
+        return this.configuration.getBoolean("settings.warn-on-overload");
+    }
+
     public boolean hasWhitelist() {
         return this.getConfigBoolean("white-list", false);
     }