I have used several plant programs over the years but I now use excel for registered plants. I always have a backup on a disc, I lost two hard drives last fall and lost lots of pictures and other info. I now have a new computer and back up anything important to me on a disc. Will get an external harddrive soon.
My seedling cross's are kept in hand written spiral note books. I have a record of every cross I made since 1996. I do them this way because I can take the book to the seedling patch when they start blooming. There's a number in the top of the PVC pipe and that number is written in the book with the cross beside it.