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/
Best Answer
Yes and no.
You can fly as high as your want in Creative or Spectator mode. However, you cannot place any blocks above y256. This is why you can't fly above y256 in MCEdit.