I've been using skim to read pdfs instead of preview. Preview on OS X Lion annoyed me because of huge startup times and some other really annoying behavior of windows and grouping.
However, I missed being able to merge multiple pdfs which was quite easy with preview. Then I discovered that skim supplies a command line tool called skimpdf that allows us to do this! It is located in Skim.app/Contents/SharedSupport/skimpdf