Solution: Put Comments (annotations) into a single spreadsheet file

Open Acrobat.
Select: Advanced > Document Processing > JavaScript Debugger...
In the JavaScript Debugger window enter

Press Enter. Close the window.
note: do this prior to each run of the batch sequence

Select: Advanced > Document Processing > Batch Processing...
Select Batch Sequence "Comments to tab-delimited file"
With the default settings the sequence will ask which file(s) to process and will put the output to the same folder as the processed files are in.

When run, the sequence displays a blank PDF (example filename: Acr568D.tmp) which can be saved as a PDF with its attached tab-delimited file.

Click on the attachments paperclip to view the attached tab-delimited file.
Select the file. Save the file. While the file uses the ".xls" file extension it is a tab-delimited file.
Open the file with a spreadsheet application. Use Save As to write it to the spreadsheet file format.

Row after row of the annotations awaiting your editing pleasure.

n.b., Incorporating selected text into an annotation is described in this post -
[url]http://www.acrobatusers.com/forums/aucbb/viewtopic.php?id=13379[/url]

The column headings are file name, name (annotation author), type, page (were the PDF's first page is zero (0)), modification time stamp, and comment (text in the pop up note).

Works for all the annotation types (sticky note, text edits, highlight, callout, text box, cloud (polygon), arrow, line, rectangle tool, oval tool, stamp (personal | defaults available with Acrobat), and pencil tool).

To perform the above the documentation and the sample sequences available from Adobe are needed.

DOCUMENTATION
Source: [url]http://www.adobe.com/devnet/acrobat/[/url]

Locate and click on the "Documentation" tab. Scroll to page bottom.
Under "OTHER" - download these files.

(1) Batch sequences (PDF, 282k) (filename::batch_sequences.pdf)
This document discusses the basic concepts and techniques of using the “Execute JavaScript” command of the Batch Processing feature of Acrobat 5.0 or later, and offers sample solutions to some of the common problems users encounter.

(2) The file "batchseq.zip" which contains sample sequences used in the Batch Sequences document .

SAMPLES
Sample sequences used in the Batch Sequences document (Windows®, ZIP, 17K) (filename::batchseq.zip)
-- ++ --------------- ++ --
Sample Sequences
1. Change Security to None.sequ
2. Comments to tab-delimited file.sequ
3. Copy Bookmarks from Array.sequ
4. Count Bookmarks.sequ
5. Cross Doc Comment Summary.sequ
6. Extract Pages to Folder.sequ
7. Gather Bookmarks to Array.sequ
8. Gather Bookmarks to Doc.sequ
9. Gather DigSig Info.sequ
10. Import Named Icons.sequ
11. Insert Bookmarked Pages.sequ
12. Insert Navigation Icons.sequ
13. Insert Stamp.sequ
14. List all Bookmarks.sequ
15. Populate and Save.sequ
16. Signature Sign All.sequ
17. Spell Check a Document.sequ
-- ++ --------------- ++ --

Location of sequence files?
(Dropping the sample sequences in (2) will do the job)

For Adobe Acrobat 7
(1) C:\Program Files\Adobe\Acrobat 7.0\Acrobat\Sequences\ENU
(2) C:\Documents and Settings\[User Name]\Application Data\Adobe\Acrobat\7.0\Sequences

For Adobe Acrobat 8
(1) C:\Program Files\Adobe\Acrobat 8.0\Acrobat\Sequences\ENU
(2)C:\Documents and Settings\[User Name]\Application Data\Adobe\Acrobat\8.0\Sequences

Be well...