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"C:\Program Files\Java\jre6\bin\javaw.exe" -Xmx1200M -Xms1200M -jar "C:\Documents and Settings\User\Desktop\Minecraft.exe"
The first target is for your javaw.exe file it's most likly as writen.
The 1200M is how many megabytes of RAM to allocae to java. You may need to check how much ram you have to know how much you can allocate. If it's too big minecraft won't run at all. If you still get out of memeory problems it probably needs more.
The last target is for your minecraft launcher file. The example is typical for a launcher on the desktop. User would be whatever your user folder is named. And the launcher may be minecraft.exe or minecraft.jar
Linux
1. Put minecraft launcher (minecraft.jar) in the home folder
2. Make a text file that reads:
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java -Xmx1024M -Xms1024M -jar /home/stoningpot/Minecraft.jar
3. Set text file as executable in it's properties
4. Execute the text file. Does not need to be in same folder since i used the whole path