If he has teary eyes, the tears may have built up enough of a permanent discharge in the groove under his eye that allow bacteria to have a party. Often cleaning below the eyes with saline and gauze helps and you can use a Q tip to apply peroxide on the skin fold below the eyes to help disinfect it also.
Note that peroxide will cause eye irritation if not careful though.
It is also possible that it has nothing to do with eyes. It may be an ear infection, which often stinks. If the smell is emanating from the mouth or jaw, he may need a dental scaling again or if he is very unlucky, he may have developed a cancer of his jaw or facial bones and an infection can set in because of this. It is very common for senior pets to need a dental at least one or more times annually.
You should really have him checked out rather than fret and worry about putting him down for a facial odour. I would consider getting a second opinion if your regular vet does not give you a satisfactory answer.
Martin Slome DVM
Centre Street Animal Hospital
7700 Bathurst Street
Tel: (905) 771-9855