For tools that no longer work with the current version of StarCraft check Outdated Tools.
For tools that have their own page, have a look at the Tools category.
This is a website that aggregates replays from Iccup, Teamliquid.net, Reps.ru and other sites. It also allows for direct uploading of StarCraft replays to share with forums, IRC, Chat programs, etc.
The classic tool for analyzing and organizing replays.
Shellextension which adds many useful features to Explorer:
- Thumbnails for maps and replays
- Additional columns in details view
- Context menu operations like extract map from replay, open replay with different SC-Versions,...
Another replay analyzer which calculates "Effective APM."
Java utility that detects some hacks that can be detected in replays.
C utility that scans replays for time-5 actions (automine).
Java utility that uses BWHF technology and has a database to check for hackers
A standard StarCraft launcher for any server. Replacement for BWLauncher.
Official launcher of the iCCup server. Contains an antihack which prevents you from cheating on iCCup, Chaosplugin, and a custom lan-latency plugin.
A launcher by Smk and hjkhjkhjk that supports BWP and BWL plugins.
A powerful map editor
(Version 2.6 was found to be more buggy and less useful than 2.5)
Basically this was one of the first 3rd party editors that allowed for many great options with custom map making. It can do almost everything that SCm Draft can do with the exception of tile modding and other terrain abnormalities.
It is mostly outdated and obsoleted by SCM Draft 2 now, but still has a few minor uses.
Protection/Compression and Unprotection
Repairs maps which have been corrupted with the intention of preventing editing.
The latest BWAI project from Brood Warai.com. It has a new interface with a huge library of AI's to choose from, including cheating and non-cheating. 
An older project of the BWAI project at Brood Warai.com. It randomly selects an AI from a large library of AI scripts to ensure variety. Currently, the modifications of the AI are limited, but the BWAPI project will allow the AI in order to micro and be able to play on the level of a human player.
BWAPI Project: 
The 7x patcher allows you to switch between different versions of StarCraft. This is useful for watching replays that were recorded in different versions of StarCraft.
You can find the 7x patcher here: http://starcraft.7x.ru/?p=files
Old executables on BWreplays.com