Age old question but I've never had a cat before

So I noticed that my new cat, I got him from a humane society in October, tended to favour his one ear. This ear he lost about half of it to frostbite (before I got him) and he was always cocking his head with that side down, or he was shaking his head and scratching a lot. I took him to the vet and they said that it was ear mites, tested and everything, didn't find any ear mites but they treated him for it anyway. A week later I noticed his ear was still very dirty, just the one, but he wasn't favouring it anymore or scratching at it. So just to be sure I took him back and was told there were no ear mites but just residue. It has been another week and his ear is still dirty. I clean it out every 2 or 3 days, and see him shake his head a couple of times but it has dramatically decreased. So I'm not sure if the dirty ear is something I should worry about? Or is it normal in a frost bitten ear? He is about 2 yrs old and long hair. He also has a lot of wax coming out of this ear.

what are you cleaning it out with?  Something the Vet gave you?  You said it's getting better, so that's good. 

Did you know that gunky ear wax in cats can actually be caused by a food allergy?   Surprising, huh? 

Anyway, I am attaching a couple of threads for your reading pleasure about ear wax: 

http://www.thecatsite.com/t/240167/ear-mites-or-wax

http://www.thecatsite.com/t/202806/stubborn-ear-wax

There are lots more threads about it.  Just search "ear wax" at the top of the page. 

Ear mites are fairly rare (but not unheard of) in healthy adult cats.  However, yeast infections aren't, and they look just like ear mite residue.  All I can suggest is that you have your vet check on that.
 

This is a long time ago - so my memory is hazy but I took in an ex stray with only one ear - no idea how he lost it -we always thought fighting - he had various names but 'One Ear' was one! He was straight off the street and had worms, fleas etc and ear mites in both ears and I treated them (and still have a bite scar to prove it). If I remember rightly the 'ear wax' with mites smells really strongly and is stickier than normal. (He had been a stray for a long time but was litter trained and humanised so he wasn't a true feral)Anyway he was always a bit lax at washing himself - especially his ears and eyes were muckier than my other cats. And he did used to play with his 'missing ear' quite a bit - which I always thought was the same as humans feeling a missing limb etc - my granddad had his toe amputated and said it used to itch sometimes.In the 4 or so years we had him he never improved his personal hygiene....(Very sad what happened to him - he was killed by some dogs that had been trained to kill rabbits - the dogs had escaped and killed 2 other cats too before they were caught. The dogs were so vicious they had to be destroyed and their owner prosecuted, fined and banned form keeping animals. I always felt guilty - thinking if I hadn't made him 'soft' the dogs might not have got him -but then at least he had a happy few years with us.)

How about ringing the vets and explaining he still has problems with that ear?  Does he have more wax in that ear than the other one?  Some cats, like some people, have more ear wax than others but they shouldn't have itchy ears.

The vet can tell if there are ear mites by looking in with an otoscope, unless the ear is so dirty they can't see properly.  A cat with ear mites often needs treating several times about 3 weeks apart as most treatments kill the mites but not any eggs.  The 3-week gap lets the eggs hatch.

Ear problems can also be caused by bacterial and/or yeast infections - my kitten had one and she needed a course of tablets to clear it up.

If the problem is just in one ear I feel that it's less likely to be any sort of allergy.

A vet check for bacteria and yeast is definitely in order. And the sooner the better.

Update: took him back to the vet and they said he was clear of all mites. They washed out his ear again. It's been another 2 weeks and the residue has slowly disappeared as well as the scratching and the wax accumulation in his fur behind the ear. They did say he had a lot of wax in his ear but didn't say why or treat it other than cleaning it out. All I know is it has gotten noticeably better!

Well, that's good news that it's better!  I guess if you want to know what was behind it, you're going to have to ask them...if they even know .  Sometimes things just happen