First things first, I'm not recommending any particular solution to these ailments in clown loaches, but what follows are things I've seen work first hand or what I heard about through friends and family. Follow these ideas at your own risk.
I'm a firm believer in preventative medicine and the best way to keep fish healthy is to keep aquarium hygiene in check and make sure as best you can that the clown fish tank remains optimal for clown fish. In other words, a stressed fish is a sick fish, so just keep conditions as constant and as optimal as you can. Also, proper clown loach care and clown loach feeding play a very big role in prevenative medicine.
Clown loaches are susceptible different kinds of diseases, Ich primarily, but also other parasites, like fin rot and velvet. The best treatment for clown fishes diseases is sometimes as simple as slowly raising the temperature (sudden changes in water temperature can do more harm that good) to between 85F and 90F for up to 7-10 days. Also, add salt to the aquarium (4-5 tablespoons for every 5 gallons of water). Do a large water change (up to 70%) every other day to remove the Ich swimming around in the water. Although the clowns are sensitive to sudden large scale changes in the water quality in the long run they'll be happier to have the water change if the Ich is gone sooner. The Ich parasites don't like high temperatures or salt water and they will start falling off of the fishes.
Make sure that you don't treat them with dye-based medicines or normal copper. The reason being, clowns don't have scales and medications will irritate them causing a layer of mucus to build up on their bodies and they may suffocate. I have never had to medicate my clown loaches, but some people insist that Kordon's "Rid Ich+" is the ONLY medication they will give their clowns and it has cured them of Ich. If you read the instructions on the medications closely they usually recommend a half dose for clown fish because of their sensitivity.
"Skinny disease" is common in clown fish. As you may have guessed, a symptom is loss of weight, but also a physical characteristic called "knifeback" is observed. The sickness is caused by an intestinal parasite called "spironucleus" (this organism is also believed to cause "discus disease"). If your clown loach is eating and acting normally, but losing weight, this parasite may be the cause. There are a variety of medications that are said to work for this sickness. I haven't encountered this problem with my clowns before, so I don't have any first hand experience. A friend of mine, who lives in Sweden, used "Spirohexol" from JBL in tablet form to cure the fishes of "Skinny Disease". Others have used Sterazin from Waterlife or Flagyl (Metronidazole) which may be more work to get your hands on since it's a prescription drug in some countries.