I give you my way with
OpenOffice 3 (Linux and Windows, Mac to try)
You just open your Gutenberg text file with OpenOffice writer.
Two steps using "Search and replace with
regular expressions"
If need be you can easily make a macro to join them.
"$" with " " put a space between the last two brackets
to get rid of hard returns and then
".*$" with "&\n"
to create again paragraph breaks (yes that's
point star dollar)
Save.
After that I insert the "purified" text into a special 9x12 cm model and that's it.