Ok here goes...
Science ones:
The Elements is stunning!
3D brain
GoSkyWatch
POMT
Molecules
Anatomy
Mitosis
Maths ones:
Math Bingo is great.
Math Rocket
Pearl Diver
Factor Samurai
Slice It!
Geometry4Kids
Mathemagics
We tried various more comprehensive apps for maths but we use The Khan Academy website (they have an app too) which is BRILLIANT for learning maths and tracks their progress and awards points etc.
I bought the '11+' series of English apps but they are crap; full of errors! We don't use it much for English/literacy, although DD is writing her book on the Book Creator, which she loves.
Geography: (when we started, DD didn't know the difference between a county, a country and a continent. The other day I read out a list of about 80 countries and she told me what continent they're on. She only got about 5 wrong!
)
iLearn Continents
Tap The Map Quiz
Stack the Countries
iGeology
National Geographic World Atlas
History:
History Maps of World
Timeline Eons
British Library Treasures
Other Stuff:
Mind Snacks has great games for learning foreign language vocabulary.
Skype is brilliant
The Swarm is beautiful in a gruesome kind of way 
Winter Tree Id
Screen Chomp is incredibly useful for drawing quick picture explanations on.
Mindjet - brilliant mind map tool
We don't have any games on there that aren't 'educational' but calling these 'physics puzzles' is stretching it a bit. DD loves them though.
Where's My Water
Cut the Rope
World of Goo
There are so many free or 69p apps that the world's your oyster, really. We did a project on New Zealand before DD went there, and there was a lovely free NZ flora and fauna app we used a lot. I usually read the user reviews to gauge whether an app is any good before paying for it. Free ones you can just delete them if you don't like them. A lot of paid apps have a free 'lite' version for you to see whether you like it.
HTH