I think this is actually how you Makefile

Makefile

CHAPTERS=book/preamble.md \
				 $(wildcard book/chapter-*.md)

CONTENTS=book/title.txt \
				 $(CHAPTERS)

ALL_FILES=$(CHAPTERS) \
					book/metadata.xml \
					book/title.txt \
					cover.png				

EPUB_OPTS=--toc -S -s --epub-cover-image=cover.png --epub-metadata=book/metadata.xml

HTML_OPTS=-S -s --include-before-body=book/header.html --include-after-body=book/footer.html

CLEAN_FILES=$(patsubst %.md,%.html,$(wildcard book/chapter-*.md)) \
						rust-for-rubyists.epub \
						rust-for-rubyists.pdf \
						rust-for-rubyists.mobi \

all: rust-for-rubyists-epub.tgz rust-for-rubyists-pdf.tgz rust-for-rubyists-mobi.tgz site

rust-for-rubyists.epub: $(ALL_FILES)
	pandoc $(EPUB_OPTS) -o $@ $(CONTENTS)

rust-for-rubyists.pdf: $(ALL_FILES)
	pandoc $(EPUB_OPTS) -o $@ $(CONTENTS)

rust-for-rubyists.mobi: rust-for-rubyists.epub
	kindlegen rust-for-rubyists.epub 

book/book.html: $(CHAPTERS)
	pandoc -o $@ $(HTML_OPTS) $(CHAPTERS)

book/%.html : book/%.md
	pandoc -o $@ $(HTML_OPTS) $<

site: $(CHAPTERS) book/book.html

code.tgz: code
	tar cf code.tgz code

rust-for-rubyists-epub.tgz: rust-for-rubyists.epub code.tgz
	tar cf $@ $< code.tgz

rust-for-rubyists-pdf.tgz: rust-for-rubyists.pdf code.tgz
	tar cf $@ $< code.tgz

rust-for-rubyists-mobi.tgz: rust-for-rubyists.mobi code.tgz
	tar cf $@ $< code.tgz

ship: all
	git push origin
	s3deploy

.PHONY: clean

clean:
	rm -f $(CLEAN_FILES)

MEGAFILE

Nice work!

site, all, and ship should probably also be .PHONY.

I might change code.tgz to

code.tgz: code
        tar cf %@ %<

but that might be over-DRY-ing things a bit.

You also have code.tgz several places in the Makefile; it might deserve a variable.