Great question - i'm all ears as well.
Currently I use:
Genius Scan: Scan single or multi pages to PDF and email or send directly to other apps. Free version as well. Fantastically helpful.
Goodreader a must for Document, PDF, PPT, Excel files. Manipulate, email, highlight, alter, etc and send to dropbox or email. Very, Very helpful.
Also kicking the tires on:
PDF Splicer - basically you can take a page from one PDF doc and add it to a second or create one from scratch with saved PDF files.
Hope this helps -