I have an RMarkdown document outputting to HTML of the same form as the below example. What do I add where to apply unique CSS ids or classes to each plot output?
You can tell knitr (which is used under the hood) with results="asis" to embed a chunk's output directly into the html. Within the chunk you can use cat to simply write a style tag including your css definitions:
```{r results="asis"}
cat("
")
```
See http://yihui.name/knitr/options/#chunk_options for details.