Scan lot of documents and output them in PDF
Solution 1:
Two answers:
1) By far the easiest/best document scanner for Macs is the Fujitsu ScanSnap series. You just insert a stack of papers, press a button, and out pops a PDF. It scans both sides of each page in a single pass.
2) To convert a scanned PDF to something searchable, by far the most reliable OCR program available (for any platform, Mac included) is the AABYY FineReader package. It is miles ahead of any other package- especially Adobe Acrobat's built-in OCR which is barely usable. This comes bundled, at no additional cost, with the ScanSnap, or you can buy it separately.
I've used one of these for several years... have scanned all of my old bills, receipts, documents, etc. so whenever I need to find something I just use spotlight and can find it in seconds.
Solution 2:
I have a scanner from Brother too. The software that came alongwith it indeed supports only the most basic functions (i.e., scan and store page(s) as PDF on your machine).
To split, merge, delete, encrypt and more, I use the command-line utility called pdftk (http://fredericiana.com/2010/03/01/pdftk-1-41-for-mac-os-x-10-6/).
It's free and can handle many complex manipulations charmingly. Look here for examples: http://www.pdflabs.com/docs/pdftk-cli-examples/.
Solution 3:
Are you looking for software-only solutions or are you also open to hardware options?
After experimenting with a few, I find Fujitsu's ScanSnap series to be ideal for this sort of thing. Its form factor makes it easy to load in sets of documents up to A4, and easily turn on/off duplex/double-sided scanning. Its output to Evernote also helps in my workflow. It also comes with some software for PC and Mac that will let you do what you described, and also adds text recognition as well to it.