Looking for some good recommendations, thanks!
There's a pretty good collection in this thread from Cross Validated:
Same goes for this Quora question. This one includes the Elements of Statistical Learning, which, though not clustering-algorithm specific, I can definitely endorse as being a very useful book:
This one seems to have some specific recommendations for applied papers:
Hi! I've recently dealt with k-means algorithm and made animated shiny app with visualization of each iteration of k-means. Maybe it will be useful for you
I have yet to find something I like. In my opinion, ISLR (Intro to Statistical Learning with R) and ESL (Elements of Statistical Learning) give the mathematical details but don't really provide much advice on what to do in practice or how to do inference on clusters. I've been playing with mclust recently and am pretty happy with the results.
In terms of just getting answers in R, you might also appreciate the Practical Guide to Clustering in R, which is fairly short and rough, but has some great example code for creating nice visualizations.