I'm digging into Notebooks and really starting to like what it's offering. It's a pretty funky combination of notes, file storage and to-do lists.
To create a daily journal in Notebooks, I can create a Notebook named “Journal”, the create a new note for each day. Within this note, I can even use interapp links to connect files in DEVONthink or even ideas in TheBrain. Local links to TheBrain don’t transfer to iOS, but I believe a web link will.
By prefixing any of my daily notes with my chosen character
(!), Notebooks wil additionally create a task to be done, and populate its smart lists with that item.
Notebooks appears to have Agenda beat in virtually every way. The only thing it can’t do that is relevant to me is save a smart search, such that I can find documents created within a certain period of time. The other major feature of Agenda is calendar linking, but that is not a big draw for me.