This is actually a difficult question to answer... Here's a few responses.
1) A technical perspective...
It all depends on how much schooling she is interested in getting... You really can't go wrong with a Kinesiology degree from a major university. A Kin degree puts you head and shoulders above the rest as far as technical training goes. However, if 4 years of University is not her cup of tea then get certified from one of these organizations...
NASM - National Academy of Sports Medicine
NSCA - National Strength & Conditioning Association
ACSM - American College of Sports Medicine
I would argue that the best one is NSCA simply because it is the most difficult certification to get and it's internationally recognized. There are easier (and cheaper) places to get certified but there isn't a gym in the country that would not recognize these three. ISSA is starting to get some good recognition (it's entirely online too), but it's crazy expensive.
2) The realistic perspective...
Not a single client has ever asked me what my qualifications are. Clients don't really care what certification you have as long as you're motivating and have the knowledge to safely achieve the goals you both set. Get a top notch certification if you want a job at a fitness club. If you plan on marketing yourself alone, get a piece of paper so you can show the one client who asks for your credentials. If that's the route for her than go here. It's completely online and completely free (no catch!)
ACT - Athletic Certification & Training Commission
The requirements to pass the test is actually every bit as in depth as the other certifications so she will get the knowledge she needs by studying the materials they provide. It's a brand new certification so there is absolutely no recognition in the industry yet. I took the test and it is just as difficult as any other certification test I have taken so don't take it lightly because it is free.
3) My issues...
In all honesty, none of the certifications have high enough standards. You can never have enough knowledge of human anatomy, physiology, and biomechanics. Most certifications barely scratch the surface of what a professional trainer should know and understand. That being said, I know some overqualified people who are terrible trainers because they have poor personalities or they have trouble explaining things to clients in a way they'll understand.
No matter what route your wife chooses, make sure she stays within her scope of practice. I've heard some of the stupidest things coming out of trainers mouths. Stuff like... "If it hurts, it means it's working. That's just normal training soreness, you'll get used to it." My favorite is... "Pain is a sign of weakness... We need to focus more exercises on that body part!" 99% of PTs are not qualified to make these kinds of statements... Do your clients (and yourself) a favor and refer them to a health care practitioner. If you help them heal from an injury by referring them appropriately, they will trust you that much more and likely refer more people to you. Make your client's your number one priority, not your pocketbook.
Sorry for the little rant, I always get a little carried away with the subject of personal trainers. I really hope for higher standards someday...
If you have any other questions I'd be glad to help.
Jon
