What, if anything, do I do to repair notched floor joists?
Gluing a patch in place like as shown below will not add much to restoring the original strength of the joist.



If you were to attach a longer piece like shown in the second picture and glue this in place for the full length of the piece a whole lot more strength will be added to the joist.



Note that if the joist has started to sag down due to the inappropriately placed holes or notches you may want to try jacking the joist back into its original position before applying the glued on pieces. 

The length of the piece that you would use is going to be dependent on an number of factors including the overall span if the joist and its top to bottom height. The material could be a variety of different things including 2x4, 2x2 or even strip of 3/4 inch plywood. You could also consider gluing on a strip on both sides of the joist. When gluing make sure to clamp the pieces to the side of the joist with good pressure to make sure the wood joints are tight.