Here's my list. It makes me and my inner child very happy that some of these have been mentioned already. These are in no particular order. All of them are super special to me.

1. Specter Challenger

2. Midnight Rescue

3. Gizmos and Gadgets

4. Riven

5. Spin Doctor

6. Kid Pix 2

7. The Geometric Golfer

8. The Lost Mind of Dr. Brain

9. Thinkin' Things

10. Sim Cinema

11. Sim Tower

12. Star Wars: Yoda's Challenge Activity Center

13. Nanosaur

14. Bugdom (all versions)

15. BeeBop II

16. Bill Nye the Science Guy: Stop The Rock!

17. bonYx 2.01

Plus several other games I can't remember the names of...

In case anyone is still wondering, yes I was a young child when all these games were fairly new.