This is not a very practical option with small negatives (35mm, for example), but it is a very powerful tool with large format.
You can use the same materials used for spotting prints - Spottone is no longer being made, but Marshall's as a set of dyes that are very similar.
Another trick is to us a colored watercolor dye such as Dr. Martin's. Using a magenta dye emulated the effect of using a higher contrast printing filter with VC paper - it increases contrast. That can be helpful in masking spots.
Dyes are also useful in making tonal adjustments in the negative such that it carries through to the print. A suggestion is to tape a sectond sheet of fixed and washed film to the non-emulsion side of the negative and make the adjustments on it - that way, if you don't like the changes, they are reversable by simply removing the second film. Also, separating the adjustments from the image in the negative by the thickness of two sheets of film helps prevent hard edges.