I usually use mp3tag. Supports pretty much every file (mp3, flac, ogg, etc) and gives a handy editing interface that you can fully customize, even with custom tags. You can also automate tag extraction from or insertion into the filenames. It's free and better than the large majority of free taggers.
I am not sure how you mean missing fields in this case, but for example, if I have an album in a directory, and only some have an artist set, then I can just click the drop down and it will let you pick from all the other files selected and apply that tag to all the selected files.