It looks like a combination of normal roots and adventitious roots on a couple of those trees. That plum is in pretty bad shape, but you can bring it back if the bark doesn't peel off any more.
Now you should use the sick tree treatment and bring these trees into a more vigorous growth. I'd leave the holes the way you have them for the time being (don't fill them with anything, these saucer shapes need to stay this way). Sick Tree Treatment
To identify that top tree for further recommendations, send a photo of the leaves and flowers or fruit or nut if there is any.
On the plum you may trim off those short roots that are sticking out from the bole above the flare. Since fruit trees are often grafted to a root stock, you need to be sure you're below the graft and exposing the flare of the root. To understand what you're looking for, this page talks about grafts
File comment: This image is from the page: http://www.ag.ndsu.edu/hort/info/fruit/graft/graft.htm . The point where the graft occured is several inches above the flare of the original stock. The graft and the flare need to be exposed.
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