What stitches are strong for clothing seams when done by hand?
Have you looked at the Alabama Chanin books? I've read only the sewing patterns one, which is meant to help readers make the stuff that A. Chanin makes and sells. It's worth a mention for the clear photos and instructions for sewing seams by hand in cotton jersey. They suggest backstitch, plus hand-sewn zigzag or blanket stitch to catch the cut edges.

For repairing a formerly serged hem, I use herringbone or straight-up cross stitch. For side seams that aren't visible on the public side, I use backstitch. Pockets are trickier because they bear weight; I follow Tom van Deijnen there and accept that some patching can be visible intentionally, and lovely in its visibility. Which sorts of seams do you have in mind?