web editors:
quanta - wysiwyg
kompozer, taken over from Nvu , still slightly buggy, can crash without any apparent reason
bluefish - most stable of them all but its not a graphical editor.
Screem - should really be taken out, as it is more buggy than bluefish and it serves the same purpose

Pre School additions:
- Childsplay and its extra packages seem to run very nicely, and kids seem to like their simplicity above gcompris in many cases.
- Linux Letters and numbers

Astronomy:
Stellarium
Celestia
earth3D - open alternative to google earth, seems to work quite nicely, although not as full featured.

Education authoring tools:
Jclic and jclic author - Create multiple choice type multimedia lessons that work directly under gnome or kde.
VYM - View Your mind (mind map tool)
Mnemosyne - Flash card system
Anki - another flash card system
Salasaga - create elearning objects that output to .swf
pdfeditor

Music:
Rosegarden
Audacity
Jokosher
Gnu Solfege - might be a good choice for serious ear music training, though it needs a midi device to be used properly.
Denemo - edit musical scores

Video:
Pitivi - video editor
Istanbul - record session of your desktop environment as its being used.

Chemistry:
Xdrawchem - 2D chemistry drawing program, includes lots of structures. And you can build a 3D model of the drawings too, though that didn't quite work for me.
Gperiodic - periodic table
chemical Calculator - simple chemical structure analyser, gives elements and their mass, molecular weight...


Programming:
- Basic-256
- Squeak
- Etoys
- Little Wizard (mouse only computer programming for kids)

Mathematics:
-CaRMetal - geometry program
-Graphmonkey - mathematical graphs and curves
- Dr Geo - More geometry, more polished than carmetal

Other:
- Klavaro touch typing - nice typing tutor with lessons, program feels quite polished
-Freespeak - translations from various open online translation engines
- Blender 
- Stopmotion
- Kivio - Visio for Linux (diagrams and the like)

Game based:
- Einstein - puzzle gaim based on 6x6 cards that have relations, and the correct layour needs to be figured out.
Gbrainy
Pyscrabble

Sports and gym training -
- Kipinä (logs routines, training data)