extract specific pages into a new PDF

• PDFSAM — pdf split and merge
• using pdftk
• using ghostview, xpdf-utils, or pdftk
• pdftools
• BeCyPDFAsm can do it

concatenate several PDFs into one

• using ghostscript (search for "pdfwrite")
• using pdftk
• BeCyPDFAsm can do it

rotate pages

• using pdftk
• using Ghostscript

cut pages in half, or otherwise crop pages in a semi-automated way

• briss
  (article + screenshots)
• PDFScissors
• PDFill
• A-PDF Page Cut — reportedly watermarks pages however

add bookmarks

• JPDFBookmarks