First of all I would make sure that you really need any programs. I tried a lot of them (Omnifocus, Things, Midnight Inbox) and most of the time I came back to using TextWrangler and text files. Then using the grep command to retrieve contexts and that's it.
It works for me as I think most of these apps lack something in some department, for example, my favorite of the bunch is Things (even though it's still in beta) but you have to enter the "editing mode" to see the notes. Basically it all came down to speed, the fact that a text file is simple to navigate with the keyboard, and the fact that I didn't fill constrained to fill in the tags or notes or titles in a particular fashion, and I just input how I see fit.

If you are interested let me know and then I can outline my "system" in more details.

Good luck! Finding the right system/application is the most important thing.

EDIT: A little question, do you need an online function/app or something that syncs with your iPhone? I don't know about the iPhone (not available in the Netherlands since all providers switched to HDSPA already) so it would be cool if you could tell me what you can sync on it and not or if you want an online solution so you don't need to sync at all. Cheers.