I think it's ok, but many of the tutorials and stuff uses javaw.exe instead of java.exe,
the first one looks a little bit weird with %APPDATA%.minecraft\bin*, and I think you should use full path to java just for safety, try this:
"C:\Program Files\Java\jre6\bin\javaw.exe " -Dsun.java2d.noddraw=false -Dsun.java2d.d3d=true
-Dsun.java2d.opengl=false -Xms2048M -Xmx2048M -jar "C:\Users\Ender\Desktop\Minecraft.exe"
The difference between java.exe and javaw.exe is that javaw.exe don't have console window attached to it.
With java.exe you get this little Java window everytime you open Minecraft, and it can get pretty annoying. You can use it for debugging though, with all this stuff, info etc.
I think you can also do it with launcher, using -cp instead of -jar, and net.minecraft.LauncherFrame, but I don't know if it still work in-game, or it only changes launcher setting without purpose.
Also, is your system 64-bit?
I don't know if it's better, but I am using Java 7 instead of 6, and maybe it's placebo effect, but I think it works little bit better, so you could try it too.
By the way, my friend noticed, that Minecraft still don't want so much memory after all, because even with Sonic's Shader Mod, it was taking only 1.6 GB from 4 GB available.
I don't know if it's even worth to try all of this, when it probably won't change anything.
If you aren't using it already, I would recommend you OptiFine, that really works and helps with framerate and graphics.
http://www.minecraftforum.net/topic/249637-11-optifine-hd-a4-fps-boost-hd-textures-aa-af/
I see a number of possible problems that may help your server run with less ram.
PlayerViewDistance
On many servers, including my own, the ViewDistance parameter in your server properties file may be too high. Decreasing this value will cause less chunks to be loaded for the players, but if you set it too low, ie below 3, then you won't be able to see far enough to have a good time playing.
This is easily fixed by decreasing the "view-distance" parameter in the server.properties file.
Command line args
I see a small problem with the one you pasted in your question:
Java -Xms512M -X3584M -jar minecraft_server.jar
I could not find a java argument that is simply 'X', although I assume that you are trying to set the upper memory limit to 3.5GB. Here is what that should look like:
Java -Xms512M -Xmx3584M -jar minecraft_server.jar
Or an even simpler version:
Java -Xms512M -Xmx3.5G -jar minecraft_server.jar
If you're willing to experiment, lower the maximum limit by 512mb every restart, and measure how it performs. In some odd cases, you may see a decrease in actual used memory.
Use Java 7
From my past experience, running on an Ubuntu server, running a Craftbukkit server under Java7 instead of Java6 used a noticeably lesser amount of RAM.
Switch to Bukkit
Although this may be an unwanted option for you, it definitely works. With Craftbukit there is a multitude of Plugins available for download on http://bukkit.org/ that help to increase server performance and lower resource usage.
Best Answer
Typically, most Minecraft servers will run not on your local computer, but on a remote client allowing everybody to connect to it, or otherwise some specialized server. Usually, when you're on one of these servers, you don't even have the capability for a GUI. Instead, you just have a terminal, which ends up looking something like this:
When the server is running like this, attempting to allocate resources for a GUI is a complete pain (although the system will usually pretend as though
noguiis there), and can (marginally) slow down your server.Furthermore, upon first launch of the Minecraft server, the EULA isn't accepted. This causes the server to force-crash, leaving no indication as to why if you just clicked it. This can be confusing to new users of the server platform, and such an action is remedied by forcing you to use the console, which can also provide valuable information in the case of a crash.
Really, it just boils down to the console being more verbose, faster, and the more supported way of using the Minecraft Server on any platform, being your home computer or a professional server hosting hundreds of people. Plus, having the terminal open makes you look 25% cooler, at minimum.