I'll be following this post, since I'm in the same situation (well, in the middle of a graduate program, having done quant classes with SPSS, which I could never grow to like, and now discovering and learning R for my research). There's a lot of great free resources out there - I've been going on a bit of a resource hunt, and gathered lots of links here: http://reganmian.net/wiki/R. Totally unsorted dump at the moment, I'll eventually sort through it, but might still be useful.

Yesterday I spent the whole day watching a Google tech talk by Hadley Wiggins (creator of GGPlot) talking about exploratory data analysis with ggplot and plyr, and replicating every single step in RStudio with RMarkdown (mix of code and text). I played with every single line, took arguments apart, tried out variations, until I understand what each piece did.

Here are my notes: http://rpubs.com/houshuang/ggplot-notes (RStudio makes it ridiculously easy to publish these kinds of documents online). There's a link to the talk, and the data, there too.

One thing I'm looking for is more information about doing survey analysis - I'd love to see a detailed walkthrough (like the file I posted) of someone designing a survey with Likert items, pilot-testing Likert items and generating scales, importing the whole survey with codebook, testing validity of the scales, doing some analysis of findings etc. I've found bits and pieces, but never a complete walk-through.