Create a Smart Album with the following criteria:
That will display all photos not in albums and not flagged. Then you can delete them from the Smart album in groups of about 100 or so with the following key combinations:
Command+Option+Delete to move them to the iPhoto Trash bin
Shift + Command + Delete to empty the iPhoto trash bin.
iPhotio is known to choke when trying to delete large number of photos a one time.
Deleting Photos from an iPhoto Library
1 - from an Event or the Photos mode: select the photo(s) and use the Delete key to move the photos to the trash bin. Then empty the iPhoto Trash bin as follows:
2 - from an album, smart album, book, slideshow, card, etc.: select the photo(s) and use the key combination of Command+Option+Delete to move the photos to the trash bin. Then empty the trash bin as above.
NOTE: deleting a photo from an album, slideshow, book, etc., with only the Delete key only deletes that photo from that item. Deleting a photo from an Event deletes ALL occurences of that photo in the library.