Bad druid tortures good druid.
I'd begin with a swarm of fire ants. Bite, bite. Munch, munch. Look at all the pretty scars all over his flesh.
Then move on to some bees, but not enough to kill him. You only want him to swell up a bit til he looks like he's gained 40 lbs of baby fat.
For a permanent reminder, especially if the good druid says something offensive to the bad druid, cut out his tongue. Besides the obvious drawbacks, it will now require the good druid to use the silent spell feat for any spells with a verbal component. This is a good way to permanently effect the good druid, while still allowing some room for a partial recovery. However, it will negate his highest level of spells.
Use a poison/venom to permanently damage the druid's eyes, or just remove them altogether. He might overcome his handicapp in some of his animal forms, but will at least be encouraged to take the blind fighting feat, and also to make up for his loss of vision with a magic item or spell.
Perhaps he "declaws" the good druid, by removing fingers and/or toes. Teeth might also be removed, leaving the good druid with no natural weapons in his animal forms, and appearing almost ghoulish to those who have to do business with him in towns. Such damage should certainly lower CHA and DEX scores permanently.
Making a necklace out of the good druid's teeth would just be a further insult, but gives the good druid some hope that he might be able to recover them.
If the treants "stretches" his bones, you might give him a +5 circumstance bonus (once he has fully recovered) to all of his future escape artist checks. It's only fair that he gain something from all his pain.
Insert rot grubs into his ears to eat his brain, just like in
Star Trek II. That was just cool. Results from the grubs might be a permanent -2 to WIS, and partial deafness (-5 to all listen checks). These can be compensated by magic items in the future. So, although it is permanent, it isn't something that couldn't be compensated for in some way.