Two invaluable online resources that have been lifesavers for me as I’ve started to work with unedited manuscripts:
A. Cappelli’s Dizionario de Abbreviature – The indispensable and definitive guide to Latin abbreviations, this online version of the Italian edition is much more comprehensive than the later English edition.
Some academic libraries (including the Bodleian) also have subscriptions to Abbreviationes Online, which allows you to search a growing database for any medieval Latin abbreviation.
Enigma – In what I can only imagine was the result of an inspired friendship between a medievalist and a computer programmer, this brilliant tool allows you to enter as much of the word as you can make out, together with a host of wildcard options, and then provides you with a list of every possible option, courtesy of Whitaker’s Words. Particularly cleverly, it allows each minim (the identical vertical strokes found in ‘i’, ‘u’, ‘m’, and ‘n’) to be entered as a ‘!’, so for example, ‘!!!!!!!ere’ spits out only three possible options (innuere, munere, numere) which you can then narrow down based on context.