Hmm
How about SimpleText? 🙂 That way, your journal/diary is saved in an "industry-standard" format (plain text), so that if you ever want to switch "diary programs," it will be easy. Also, SimpleText is, of course, free.
You could either have one big diary text file, or you could have your own diary folder with one file per day/week/month/whatever. Just use OS 9's built-in Encrypt function to encrypt the file(s) when you're done editing them. When/if you switch to OS X, in the event that you choose the multiple files approach, you could simply save them all on an encrypted disk image.
If your diary/journal is something you want to share, you could write it in HTML (perhaps with the help of a free WYSIWYG editor like Netscape or Mozilla Composer) and use HTML links and targets to make the journal easier to navigate.
Alex