In Game Mod Manager - 28 November 2011 - Minecraft files

Installation instructions Read very carefully!

Video instructions for Mac OS X, courtesy of DrRedstoner:

Open up your Minecraft folder. On Windows, type "%appdata%\.minecraft" into a run dialog box. On Mac, the folder is "Library/Application Support/minecraft". On other systems, it's ".minecraft" in your home directory.

Open the bin folder inside your Minecraft folder. Delete "META-INF" from minecraft.jar. Rename minecraft.jar to game.jar.

Finally, click the link above the download. Place the downloaded file (minecraft.jar) into your bin folder.

After you log in but before Minecraft actually starts, you will see a screen that allows you to enable and disable mods. When you're ready, click the "Start Minecraft" button to play Minecraft with the mods you have enabled.

Use
After you run this game with the mod manager installed, it will create a folder called "externalmods" in your Minecraft folder. You can put mods in there. The mod manager will load .zip and .jar files, and regular folders. It will also create a configuration file called "modmanager.txt". If you want to change what folder mods are loaded from, you can do that in the configuration files. On Windows, you need to use two backslashes to separate folders, not one. Sorry.

Mods need to have the files that would normally go into minecraft.jar in the first level of the .zip or folder. For almost all mods you can install them just by downloading them into your externalmods folder. If the mod has a "Put in JAR" folder or something similar, then make a new folder in your externalmods folder for the mod, then copy the contents of the "Put in JAR" folder into the new folder.

The order of mods in the list is the order they will be loaded in. Most of the time this won't matter, but if one mod needs to be installed before another, make sure it is loaded after (I know this sounds backwards).

Using ModLoader
ModLoader will normally not load mods that appear in the list. This is, however, very easy to fix. Download this modified version of ModLoader.class, and replace ModLoader.class in ModLoader.zip with it. Be sure that ModLoader.zip and all of your ModLoader mods are being loaded by this program. Only for 1.0.0, sorry if you need a different version of ModLoader.