Man, use Org mode. I am on it for over a year now, best experience ever. Nice community as well, lot's of add-ons (like Org-mode based blogs, ical exporter and so on). Give it a try.

Regarding my setup: I have one big Org-mode-textfile and everything in there. I have a folder with additional text-files like journal stuff and the like. Everything on version control. Contacts (you can use the apple adress-book with emacs) and email the Apple way. Scripts do backup all this on dvds. One of these discs is in my brother's house, so even in case of fire...

There is a program Mac Notetaker or so, it is basically "use your emacs files on your palm pda" kind of thing. It is free software. I used it when I still had my palm active.

I switched to text-files and emacs precisely because of the issues of long-term compatibility. I will never have to change software again. It is a cool feeling. One warning however: you end up tweacking your emacs config a lot. The time you save by not checking out all those hot new shareware-utils, you easily loose in emacs hacking.