Labor Economics

David Card's Notes

Enrico Moretti's notes aren't publicly available, but his class has some overlap with David Autor's Labor courses.

Public Economics

Alan Auerbach's Notes

Emmanuel Saez's Lecture Slides

Raj Chetty's Lecture Slides

Applied Econometrics

Ken Trian's Discrete Choice course

Train's textbook is also quite clear and useful

Pat Kline's notes for applied econometrics are fantastic, but are not publicly available. Notes from NBER's What's New in Econometrics are a decent substitute.

Alex Rothenberg's Graduate Student Instructor Notes 

These are great, comprehendible notes for the 3rd quarter of the Berkeley graduate econometrics sequence in the first year. The notes review classical least squares, GLS, SUR, Heteroskedasticity, Serial Correlation, Panel Data, Endogeneity, IV, 2SLS, and introduce both time series and nonparametrics.

Macroeconomics

David and Christy Romer's Macroeconomic History Course: Empirically oriented & quite topical.

Yuiry Gordonichenko's Applied Macroeconomics: Very useful class, but unfortunately the notes aren't publicly available.

Demian Pouzo's Dynamic Programming Course: Notes aren't publicly available, but the course follows Stokey and Lucas closely.

Courses by Maurice Obsfeld and Andres Rodriguez-Clare may also be of interest, but only syllabi are available.

Here is an old outline that I wrote for incoming graduate students to give them a sense of what material they'd be covering in the first year at Berkeley. It may be a helpful resource for those who are curious what the first year of an economics Ph.D. program entails.