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Alternatives for command line
Customize the DOS-box and/or Run dialog... what's there to do ?

If you'd like the option "Command Prompt from here" added to the rightclickmenu, check here. Enhancing the run box with your custom commands (?!) - take your pick ;). At this page, some complete replacements of both the DOS and run box:
 
Replacing the DOS-box
Ok, that was just a system tweak, how 'bout some decoration... there's more to this, but eConsole (free) is a real decorative replacement/enhancement of the DOS-box. It supports background images and transparancy. Latest release also supports docking, and more. Long time since last update.

Marko Bozikovic created Console (free, Win NT/2k/XP). Inspired by eConsole, and though not working in 9x, adding some enhanced features (more stable, faster, very configurable and supporting alpha transparancy). Very nice!
With it being open source, nivenh worked with source and released Console 2 - "Text aliasing and shadow options added among other small tweaks."
There's also an old Console (free), a skinnable and free replacement for the DOS-box. An oldie, but still working, even in XP.
Replacing the Run dialog
OverRun (free, Win 9x/NT) is a replacement for the Run dialog. Title, message and icon can be customized.

Less customizable, but offering some enhanced features is RunModule (free, Win 9x/2k). But looks different nonetheless.

And there's dRun, by d e l u s i o n a l 1 3, another cool looking, small run dialog - very convenient.

Then, Consolable (free) is a command line replacement, small and convenient. Skinnable, that's a normal and hiding version, quite simple but a powerful little thing!

"Run+ is basically a better run box. It sits in your tray, and when clicked pops up with a text box for you to type your commands into. It has all the features the run box does, but also supports small 'scripts', 'shortcuts', multiple launches, terminating apps, and a few other nice features. The UI is completely customizable, and the tray icon can be changed easily (extra icons are included)."
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