Currently building my own database in Filemaker for storage of all references I find on my research names (whether the data is unlinked or linked). From this data I maintain the pedegrees in Reunion. I am contemplating adding Journaling to my database since like you I can't find a suitable way of doing this in Reunion. Maybe v10 will have something.
Am also exploring using Notebook and Scrivener for notekeeping. I have Filemaker, but have not used it for journaling as of yet-- am interested in how a good template might be developed to accompany Reunion. Otherwise use Open Office's word processing feature. Basically I use the notes feature on Reunion for archival extracts.
I'm looking at Notebook too, but haven't set anything up for genealogy research journaling. How do you like it? I'm not really a Filemaker user, but that is a thought. I have a simple Bento db for maintaining my documents and paper-filing records, as I have so many oversize and strange materials that I need to know what they are and where they are physically stored. Many don't fit neatly in file cabinets, and my space is very limited.... But setting up journaling is really a tough one for me, and I need to do it.... I'm not that disciplined, I fear.
Circus Ponies Notebook is good for making lists and ToDos. You can add any number of pictures, documents made on programs like Word or pdfs. I have a page for maps. I have scans of newspaper clippings and things I have downloaded from Ancestry.com or Rootsweb. There is not much you can't do with it! I can transfer things into Reunion in notes or multimedia, too.
Ouch! That's a painful process. I recently migrated to Reunion from Legacy (mainly because I hated having to open Windows on my Mac just to use Legacy), but was able to import a GEDCOM from Legacy without too many problems. There is always a little cleaning up to do though. Good luck with your transfer.
I'm in the process of transferring everything over to Reunion on my Mac from FTM on my PC. Doing it slowly and manually due to duplicates and errors in FTM.