Handwritten notes on the T-1 can be saved on a desktop computer easily. When writing the note, simply press the button on the far right of the T-1, and then
Capture Screenshot.
An image of the note is saved and is visible in Multimedia >> Pictures on the device itself.
To save these on a desktop computer, simply connect the reader and open with a file manager. The pictures are stored as jpg files in this directory: Sony PRS-T1 > Sony_Reader > media > images > snaphw.
The Sony Reader software saves notes, too, but you may prefer a local copy, like me.
The jpgs are static, of course, so they can't be modified again in the reader. Also the original dates the notes were written are not retained, only the dates when the screenshot was made.