There are key components to a good hidden seam...
-Practice, practice, practice stitching
-When you do the Ladder Stitch don't "Over Pull" the fabric. Many people will pull too much causing the fabric to bunch up a bit. Thus causing the stitch to be seen.
-Work and Pull- when you do the ladder stitch you'll want to do about 10 stitches, pull together, then continue. I use to do a huge line of stitches and then pull- which can cause a tangle and then the stitch won't gather.
-Use strong thread- sounds stupid but if you purchase cheap thread you'll regret it. Sometimes you'll have to put some force when gathering your stitch. Early on when I started building I found the thread breaking...causing all my work ruined. Use strong thread and the chances of this happening are next to nil.
-I recommend using a needle to pick the seam first, then move to the dog brush. A warning with the dog brush: If you are brushing out a seam try to brush the entire puppet face (with the seam) because the area you brush (the seam) will begin to look more worn or the pil will be greater. This might bring more attention to the seam. By combing the entire puppet face sometimes you can stop this from happening.
-I don't recommend toothbrushes- use your sewing needle instead.
-Sometimes you have to realize that the seam (no matter how hard you try) will show. The pil on fabric has to be a bit high to do a somewhat normal hide of a seam. Many fabric stores are selling Anti-Pil fleece so make certain the material you are purchasing isn't going to fight against you.
-Your eye will be able to see the seam but camera's won't- I recommend taking pictures as you build. Some seams I've done I can see until I video taped them and the seam magically disappears! Now with High Definition camera's you'll have to worry, but usually for Youtube videos you'll be fine.
-My last point is ...who cares...ya, I said it...LOL who cares that you can see the seam. Remember that the character is what is important! If the character is good- people will not notice the seam. The puppet building community might care about them but the percentage of us is very small compared to the rest of the world who won't know what to look for. Seams are nice to have hidden, but sometimes not necessary.