Indiscriminant use of antibiotics is why we have so many resistant strains of bacteria today. Improper use (such as too low of a dosage, not giving enough dosages, or too frequent use) makes antibiotics relatively ineffective. That's why stronger and stronger antibiotics need to continuously be used! Don't believe me? Look at tetracycline. It is hardly ever used because WAY too many infectious bacteria now have resistant strains!
>>Well I hate to say it but you need to take a very thorough look at the next pile the snake leaves[I know...lots of fun]. What I suggest you keep an eye out for is mucousy/cheezy stuff within the sample. It is usually white, clear, or greenish. That would make me lean more towards a bacterial infection, which Panacur and Flagyl won't do much for.
You are correct on Panacur (use it to treat things like internal worms), but incorrect on Flagy. Flagyl IS an antimicrobial. (It has some other uses, too.) It and Baytril, for example since you mentioned it, are both in that group. They just are used to treat different microbes along the spectrum of anaerobic to aerobic, gram positive versus gram negative, etc.
Additionally, some species (tricolorted kings, indigos, rattlesnakes, etc.) are very senstive to Flagyl. I'm nervous about EVER giving Flagyl to a milksnake. No real problems yet, but I've seen what happens giving them a standard dose. It can be ugly.
>> A fecal exam is a good idea,
I agree. If you can't do it yourself, fork over the money to have a vet do it before you start treating it yourself. THAT is the best advice anyone can give you.
> anti biotics like Baytril which must be injected.
You can get and use oral Baytril, also. Since injectable Baytril can cause local necrosis, there are some definite benefits to using oral Baytril. Baytril can be VERY hard on the kideys, so be careful of where you inject it. Also don't use the injectable Baytril for more than a first few dosages - switch over to oral Baytril if you need additional dosages.
> I feel the most thorough way to find out if a snake is "perfect" is witha cloacal smear.
For anyone interested, remember that some pathogens are infrequent shedders, so a "sick" animal maye appear clean on MANY fecals since the pathogen isn't entering the feces. Then BOOM, it is all over the feces for a couple shots. Then, no more. Rinse and repeat. Crypto, for example, is a sporadic shedder. Stomach gavage is the best way to test for that one, but even that isn't 100% reliable.
> It would not hurt to run some of the parasite type meds you have through it.
But they can inhibit appetite. In a sick snake, this can be a BAD thing if the medication isn't actually needed.
> Panacur is especially forgiving if the dose is not perfect.
Very.
> My vet swears by Baytril for use outside his office.
Too many of them do that as a "blind treatment." Not saying your vet is in that group, but if they are: find a better vet.....lol.
> He swears Baytril is a wonder drug. It is VERY effective.
I used to laugh and call it a super-drug. "If Baytril didn't kill it, nothing would." All in JEST, of course, since I am STRONGLY against shotgun treatments. However, I was unlucky enough years ago to run into a strain of bacteria that was resistant to baytril. Should have worked, but didn't. Whether it was due to the improper use of Baytril by people, I don't know, but it WAS a resitant strain. I sure as hell hope it has died out. I lost about 10% of my animals, it was airborne so almost EVERYTHING showed clinical signs, and the meds cost an arm and a leg for us to purchase wholesale (no vet mark-up). Had to clean cages with a special cleanser (bleach AND Roccal-D weren't doing a good enough job), etc. Not pretty. Lost an adult male P. ruthveni to that bug, too. 
Don't rely on it to heavily. I would also STRONGLY discourage the use of Baytril in African House snakes. They seem to have a greater level of sensitivity to it than any other snake I've ever given Baytril.
KJ