The Voynich Manuscript folder on my desktop is divided into subfolders, one for each section. These contain subfolders for each folio, plus one for General Files.
Other folders are General Files, Folio Scans, Transcriptions, Papers, Uploads and Current Research Files.
I use MS Word 6, and Open Office 3 if I’m on my notebook.
WordFind 3.3 handles word lists, palandromes, and anagrams. Other lexicon files can be added, and it returns results in several optional formats.
For graphics file viewing I use IrfanView, which will handle just about any format, including .sid, which is the format for the high-res VMs scans.
For graphics creation I use Paint.NET, an art program that is simple to use, has lots of support, and many useful plugins.
For astronomy and astroarchaeology I have Starry Night Pro 4, long since superseded, but perfect for my work. It handles precession, as well as being able to add objects like comets and asteroids. It handles the 1582 calendar change by deleting those eleven days.
For astrology I use StarFisher 0.8. It’s not a subject I know much about, but since at the time of the VMs astronomy and astrology were the same science, it has proven to be useful on occasion. It does not address the calendar change, which makes the results confusing if I forget.
IrfanView, StarFisher, WordFind, Open Office and Paint.NET are all freeware. I don’t have links handy, but they are easily found.