The situation was that I needed to compile a flex application on a server since it was going to be using a different services-config.xml than the instance on my laptop. Anyway, I got sick of typing the flex compile commands so I wrote a quick batchfile that you can modify. Just save it as CompileAppName.bat and click it from windows!
@echo off
START C:\flexsdk\bin\mxmlc.exe -file-specs=E:\websites\yoursite\web\main.mxml -output=C:\websites\yoursite\web\main.swf -services=C:\JRun4\servers\cfusion\cfusion-ear\cfusion-war\WEB-INF\flex\services-config.xml -show-binding-warnings=false
EXIT
First use start to call the compiler (you will need to change this to wherever you put the Flex 2 SDK).
-output is the command that specifies where to put the compiled swf.
-services is the command that specifies where the services-config.xml file is on your jrun server (in my case to connect to ColdFusion).
-show-binding-warning is because I'm bad and I have a binding warning in my code and I didn't want Flex to tell me about it. Exit simply closes the CMD prompt once it's run. Easy huh?