Hehe, here goes

You might have read it on my blog, but maybe you can add links or something to programs/files like,
Metaex.exe
Metaex Manual
Mach1.met.txt
Modding Manuals -> Which i'm going to polish up)
Hamachi
mIRC -> Java Applet?
Jeballi's Walkthrough(steal it but give credit

)
And Maybe you can add Minigames(it is GAME-maker after all, pong will be nice xD

)
For the Program:
Add a "Sound on/off" button
Create a better "Description" window(this one is kinda messy)
Repair the "Launch Machines" button(crashes with me, at the N)
Change "Loading screen" with something Machines-like
Change Program Icon (not that default GM icon)
Different Backgrounds
Change "Jouse Mod" to "Joust Mod"
Highly Optional
Add a Skirmish Manual(which i'm going to create: A picure of minimap with small description, through which you can scroll

)
Add a "Scaled maps" download center(Which I'm scaling and giving to you, but maybe this can take too much space...)
Enough to keep you busy I hope

Now let's see what the next person wants to add
