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As always there is a complete lack of theoretical CS courses.

There's one on Coursera taught by Jeff Ullman but OP said he avoided adding stuff you can find on MOOC's.

The whole Algorithms section is theoretical CS.

There's a lot more to TCS than algorithms.

Furthermore, the most theoretical course there is the Princeton one. The rest all focus more on using algorithms to do things than on theory.

Can you recommend some courses?

This is mostly from a theoretical crypto perspective since that's what I'm interested in:

Introduction to Cryptography:

    Yehuda Lindell - http://u.cs.biu.ac.il/~lindell/89-656/main-89-656.html
Complexity Theory:
    Jonathan Katz  - http://www.cs.umd.edu/~jkatz/complexity/f11/
    Luca Trevisan  - http://www.cs.berkeley.edu/~luca/cs278-08/

Foundations of Cryptography:
    Yehuda Lindell - http://u.cs.biu.ac.il/~lindell/89-856/main-89-856.html
    Jonathan Katz  - http://www.cs.umd.edu/~jkatz/gradcrypto2/
Secure MPC:
    Jonathan Katz  - http://www.cs.umd.edu/~jkatz/gradcrypto2/f13/
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