For every mod tool, if there are instructions, they are included in their respective readme files. There is no assurance that these versions of the tools are the latest ones - check Planet Elder Scrolls, the Official Forums, and the authors' sites for the latest version.

Although there are many fantasy name generators already on the net, our own tool makes names based on those found in Morrowind files. It uses an implementation of markov chains that selects parts from random names to generate new ones.
Name Generator.

TESAME, or The Elder Scrolls Advanced Mod Editor, is a tool that helps in cleaning mods out of unwanted changes to cells and merging them. Cleaning mods is one of the requirements to get a claim passed, so make sure you have not accidentally changed some random tree's location that doesn't have anything to do with this.
TESAME has been created by Erik Benerdal.
Download TESAME.

TESFaith is a command-line program written by Paul Halliday that moves entire cell blocks to another location. If you have accidentally made your landscape on a wrong cell and don't feel like doing it again, this is the tool to use. The newest version handles door teleports as well.
Download TESFaith.

Previously, textures in NIF files (that morrowind uses for 3d models) had to be changed with a hex editor. NIFTexture is a tool that makes this much easier - all you do is select a NIF file and then select a texture to apply on it. It also has additional features like changing tint color and editing multiple files at once.
Dave Humphrey's homepage.
Download NIFTexture.

Overunity is both a mod manager, like Morrowind Launcher by Bethesda, but more importantly a mod packager. It finds out which files are being used by a mod, allows one to move them to a secure place and checks for shared dependencies with other mods.
Shanjag wrote Overunity.
Download Overunity.

Leveled List Merger does exactly what the title says - merges leveled lists of two plugins. Unless merged, only the most recent list will be used, and any other plugins will fail to work as supposed to.
If you want, you can try to contact Horatio, the creator of LLM, although he is not active in the community anymore.
Download Leveled List Merger.

Many modern games utilize the DirectDraw Surface (DDS) format to have a standard and neatly packaged file for the texture, all of its mipmaps, compressed or uncompressed pixel formats and all kinds of technical details you don't really have to worry about. Morrowind utilizes this format and in order to save graphics to .dds, you need these tools. In their original packaging, most people will only need the Photoshop plugins.
Made by nVidia, according to Microsoft's specs.
Download DXT Tools.

GenMod is an automatic random interior generator that supports most of the architectural styles shipped with Morrowind. While this tool can be helpful, it should certainly not be used exclusively in making interiors - it doesn't magically do all the work for you.
Jim Adam's homepage.
Download GenMod 3.1.

As opposed to genMod, mGen creates exteriors automatically with a ruleset that the user can change. Terragen is commonly used with it to create terrains that mGen can load. Neither mGen should ever be used without working on the mod by hand as well.
Download mGen-0.2.zip.

A tool that allows one to load NetImmerse model files to 3D Studio Max 4 and 5. It's very unstable, as said in the hosting site. Installation is simple: copy the file to 3dsmax's \plugins\ directory. After working on the NIFs, delete the plug-in to make 3D Studio Max more stable. Here is a tutorial for using this plug-in.
Download NIF Importer 3DSMax plug-in.

Dave Humphrey's 3D Studio Max NIF plug-in is able to import mesh data, textures, groups and hierarchies and material properties of .nif objects to 3D Studio Max 4.0. It is not able, however, to do anything beyond that like animations and stuff.
Download NifPlugin v0.11.

TESDTK is a tool that can remove master file dependencies from a plugin file. Everything from dependencies on other .esp files to Bloodmoon.esm or Tribunal.esm can be removed, which makes it a great tool for everyone who wants to take a look at plugins that requires masterfiles they don't have.
TESDTK requires the Java Runtime.
Download TESDTK.

If you have any problems with stuttering or laggy sound, it might be because your video card or other PCI/AGP devices have too high a latency that doesn't leave any bandwidth for the sound card. PCI Latency Config fixes this problem. Set your sound card's latency a bit higher and video card's latency a bit lower. If you have other devices that have high latency but are not that important while playing a game, you can tinker with them too. The general rule is to just give a higher number to the sound card and a lower one to the video card. This should not have any effect on rendering speed.
Download PCI Latency Config.

In case you can't cope with nVidia DXT tools, you might want to try the DDS Converter 2 which is a very simple program for converting textures to .dds format. If you don't have Photoshop, you might want to try this instead.
Download DDS Converter 2.

You will need this if you want to do Oblivion modding. It requires latest DirectX 9.0c (February 2006 or later) to work properly. You will also need to download the latest patch from Bethesda's website and update your Construction Set to fix several key features.
Download Oblivion CS (Bethesda site).

The TES4 Plugin Utility will merge two or more plugins into a single plugin, convert a plugin to a master or a master to a plugin, edit the plugin description, and display/copy plugin records.
Download TES4 Plug-In Utility.

A graphical program that allows you to open NIF files, view their contents, edit them, and save them. You can use it to quickly make changes to specific properties of a NIF file such as changing the texture, adding translucency, and more. You can even create texture templates, and import & export OBJ files. Before NifSkope there was no trustworthy way to get new models or textures into Oblivion and sometimes Morrowind. Strongly suggested if you ever plan on messing around with models or textures!
Download NifSkope.

TES4Gecko works with The Elder Scrolls IV: Oblivion plugin and master files (*.esp/*.esm). It is designed to let mod-creators manipulate plugin and master files in ways that Bethesda either did not imagine or decided to leave out of the official Construction Set.
Download TES4Gecko.

Even though there's a total lack of information on this tool, it is loved by many. It is a low-level editor for Elder Scrolls III: Morrowind game files. It can edit .ESM files (master game files), .ESP (plugin files) and .ESS (savegames).
Download Enchanted Editor.