Does anyone have any experience with or knowledge of anyone who has filed an Article 138 UCMJ?

My recommendation would be to see the IG. Couple reasons I say that is:
1. While the UCMJ and manual for courts martial feels like an easy read; it isn't. Preface your concerns with "I believe" the Commander is doing x and think it's under 138. Here's the documentation that backs my belief. Let the IG figure out what article supports or doesn't support your perception.
2. The IG pathway gives you some cover from overt retribution if you're incorrect in your perception. I was always a chain of command guy, but in instances of perceived wrongdoing and potential UCMJ action against a field grade officer or higher in a command position is a sensitive issue and you need your ducks in a row. As a CSM if a Soldier brought an accusation against a Commander to me that would be my first phone call.

It's good that you are asking the question here before moving forward. There are many outstanding SGMs and others who can offer great advice and mentoring for you. Please do your research and listen to the Senior NCOs on this. I would recommend 1. trying your chain of command and if necessary seek approval to jump chain to any point where you feel you can trust. 2. seeking advice here and within your post from senior NCOs. 3. If 1 and 2 fail, contact your IG and be ready to defend yourself with documentation and credible testimony.

As Col Joseph Lenertz pointed out, documentation is key when going down this path. You will learn as you continue in the military that more weight is put on to have paperwork as you continue up the ranks and after. As a NCO, I carried a Leadersbook, as most do. I had everything within that folder not just for me but for my troops. It made getting things done from discipline to awards so much easier. Rather than scrambling to come up with bullets for their awards, I had it and thankfully due to the mentorship of senior NCOs who showed me how powerful a good Leadersbook could be I have carried that into civilian life. Today, I maintain a "LifeBook". Inside I keep things like my current lease, to my dog's paper work, children's report cards, military paperwork and other things that I find I'm asked for.

Whenever you are thinking of going down this road, you'll need that level of documentation because the last thing you want is to move forward without the proper background work which will result in setting yourself up for failure.

Bottom line up front..
NO, never seen this art used

An Article 138 complaint is a formal complaint against a Commanding Officer (rank immaterial). Any member of the Armed Forces who believes he/she has been wronged by his Commanding Officer and the Commanding Officer has refused redress, may complain to any supervisor commissioned officer, who forwards the complaint to the officer exercising general court-martial jurisdiction over the officer against whom it is made.
Before you can submit an Article 138 complaint, you must request, in writing, that the CO address the wrong. The CO must act upon this request for redress in a timely manner (not specified, so say 30 calendar days) and notify you in writing of the action taken.
The Article 138 complaint may address a large range of subjects but does not include issues like UCMJ, NCOER (OER) as those have specific methods and avenues of redress.

I have personally filed on Art. 138 on a 2-star because of and unjustified and unsubstantiated performance evaluation. It worked out great for me and the evaluation was purged from my record. Factual documentation is key and also ensuring that you take all emotion out of your complaint.

From the IG Desk: "ART. 138 of the UCMJ: Complaints of Wrongs" is a powerful tool in addressing and correcting a 'wrong.' It is NOT to be taken lightly, or used as 'pushing all the buttons' to stir up support for a perceived local issue. I counsel that it should be considered only as a last resort, after other more common (and successful) avenues have been attempted. If in doubt, make an appointment to see your local IG for assistance. It's always best to attempt resolution of any problem "At the lowest level possible" before contemplating use of a tool such as Article 138 UCMJ. Why? Because this action may become a permanent part of a senior leader's record through no fault of their own.

Consider: "Any member of the armed forces who believes himself wronged by his commanding officer, and who, upon due application to that commanding officer, is refused redress, may complain to any superior commissioned officer, who shall foreword the complaint to the office exercising court-martial jurisdiction over the officer against whom it is made. The officer exercising general court-martial jurisdiction shall examine into the complaint and take proper measures for redressing the wrong complained of; and he shall, as soon as possible, send to the Secretary concerned a true statement of that complaint, with the proceedings thereon."

That "Secretary" is the Secretary of your Service, such as "Secretary of the Army" or another branch. Ensure your issue is worthy of such lofty attention before you invoke Article 138.

The following URL link offers a good explanation: "http://girightshotline.org/en/military-knowledge-base/topic/grievances-article-138-complaints"

Under Article 138 of the Uniform Code of Military Justice, any member of the armed forces who believes himself or herself wronged by his or her commanding officer may request redress. By requesting redress the wronged member of the military is asking that the “problem” be addressed and fixed. Army Regulations [1] define a “wrong” as:

A discretionary act or omission by a commanding officer, under color of Federal military authority, that adversely affects the complainant personally and that is-

(1) In violation of law or regulation;
(2) Beyond the legitimate authority of that commanding officer;
(3) Arbitrary, capricious, or an abuse of discretion; or
(4) Materially unfair.
If the problem is not addressed and fixed by the commanding officer, a formal complaint (Article 138) can be made to a superior officer (higher in rank to the officer who is responsible for the problem). This will trigger an investigation into the problem by the court-martial convening authority over the commanding officer against which you brought the initial complaint. The investigator should, “examine the complaint and take proper measures for redressing the wrong complained of” [2] and should report their findings to the Secretary of the Army (or Navy, Air Force etc). Any retribution or reprisals for filing an Article 138 can be the basis for additional complaints.

Before you file an Article 138 Complaint:

The actual filing of an Article 138 complaint will go on the officer’s official military record and thus the actual filing is not something to be taken lightly. Even before you request redress, which always comes before you file an Article 138 complaint, consider orally conveying to your chain of command that you are contemplating submitting an appeal for redress in pursuit of an Article 138 complaint. One option for this is to use the open door policy to meet with your commanding officer. In a polite and formal tone you could suggest something similar to the following:

Sir/ma’am, I have been trying to resolve __________ and I know I’m being harmed by __________, and I am thinking of filing an Article 138. I know this is really serious, so I just wanted to speak with you first and see if we can’t work something out.

Before you file a request for redress or an Article 138, we suggest that you call the GI Rights Hotline at [login to see] .
http://girightshotline.org/en/military-knowledge-base/topic/grievances-article-138-complaints

I saw it once ...
The bastards circled the wagons and tried to crucify the Lt who filed the Charges... Until the Senators got involved... the bastard was relieved, Promoted and assigned to Ft Greeley Alaska....

A 138 complaint can be a useful tool, if done correctly and for the appropriate reasons. I would encourage you to review AR 27-10 Section 19 to familiarize yourself with the process.

In any case make damn sure you have some firepower in your corner. I was lucky enough that my flight to AIT was the same flight that the former commander of 3/69 armor was on. 3/69 was yhe spearhead into Baghdad airport. I met him and he gave me lots of advice and is one of the shining examples of how an 06 should be. Hes kept up with my career and i talk with him from timeto time.