So the Sand-Resistant (PVD) coated mags that come standard with the M9A1 are supposed to be the most reliable mag according to Beretta, in part because of its anti-friction follower. They're also the most expensive that I can see.

Are these really that much better than the standard black finish mags found here? http://www.berettausa.com/en-us/beretta-92fs-magazine-9mm-15-rds/c86021/ I don't mind paying a bit more for a quality mag but is there any data out there that illustrates in the real world that the PVD mags are that much better than the standard Beretta mags, or for that matter the Mec-Gar mags for Beretta? Anybody with experience with these?

I've used just about every Beretta OEM magazine (standard 15 round, 15 round PVD, 17 round) and I have no issues to report.  I'm not sure the PVD magazine offers any advantages (outside of a desert environment) that justifies the increased cost.  

The only M9/92 series magazine I've had problems with is Check-Mate.  Two Check-Mate magazines (pre-2005 date stamp) proved problematic and would fail to lock-back the slide when empty.  Check-Mate was responsive and replaced both magazines, but I wouldn't use them in for carry.  In some ways military issues with Check-Mate magazines in Iraq are the reason the PVD magazines were designed.

I've used the Mec-Gar 18 round magazines and I've had zero problems.  The Mec-Gar magazines have the endorsement of some knowledgeable Beretta users (Bill Wilson, Ernest Langdon).  If you look around you can find them for $20.  Given the choice I'd buy and carry the Mec-Gars, but all of the Beretta OEM offerings are excellent.  

Looks like Beretta will release a 17 round PVD magazine with the M9A3...might be the new heat.

If you don't live in a desert, then no. Even if you did, keep the gun clean & not abused & the answer is still no. IMHO
Have you seen the condition of Military guns?  
I buy the 17rd Mec-Gar's or the contract plate baseplate mags form airtronics or checkmate. Never a problem with any of those.

I have a few since I previously owned a couple of M9A1s. As others have stated - there really is no functional difference outside of the desert

Just go with the Mec-Gar 18 round with the AFC .

I’ll admit it, I drink the Cool Aid on these.  A reliable pistol is really a system consisting of the pistol, the magazine and the ammo.  They all need to work together and the more reliable the individual components are the more likely it is the pistol will function when needed.  

It’s not just the PVD coating that makes them sand resistant, it‘s the new geometry of the box and removing the hole for the old heel style mag release.  In fact, the first batch produced didn’t have the PVD coating at all.  They only applied that after the Marines asked if they could make them more resistant to rust.  Blued “sand resistant” mags were sold into the surplus market.  CTD and Sportsman Guide both had them for sale.

The groove down the side of the PVD magazine creates a ridge inside the mag, which is what the cartridges ride against.  This does a couple of things.  First, it decreases friction on the cartridge as it rides up the inside of the mag during use.  The Beretta 92 series 30 round magazine has the same groove to assist in lifting the heavier bullet column.  Second, since the side of the cartridge isn’t rubbing against the inside wall of the magazine the grit and dust that find their way into the magazine now have a place to go as the bullet column rises.  Less friction and less interference from debris make for a more reliable magazine.  Removing the legacy mag release hole in the bottom of the mag eliminated a place for junk to enter the magazine in the first place.  The PVD coating is really just slippery icing on an otherwise well designed cake.

I’ve compared the follower side by side to a more or less current factory blued mag and there is a slight difference.  I don’t believe anyone could tell the difference between them if they weren’t side by side in front of you.  Just to see what would happen I’ve swapped followers and both mags ran fine.  I’m sure there’s a point to the different follower but I have no idea what it might be.

The PVD mags are maintainable.  This may or may not be an issue for you but I like the fact that I can keep these running the rest of my life if need be.  Beretta sells spring kits and Wolff sells mag springs for Beretta factory mags.  Mecgar does not sell standalone magazine springs and you can’t use anything but their spring and follower in their magazine.  While we’re currently in a pretty good place with regard to owning full capacity magazines that certainly hasn’t always been the case and no one can guarantee it will be in the future.  Again, I like the fact I can maintain them.

Mecgar mags are fine.  They have the reputation they do for good reason and generally offer a higher capacity then the factory mag.  The standard Beretta 92 mag is also a very good mag.  It offers reasonable capacity, it’s reliable, durable, maintainable and for a factory magazine pretty darn inexpensive.  I think the PVD mags are technically a better magazine.  If that means they’re worth the premium price Beretta asks for them is up to you.  They are to me but I haven’t paid retail for any of them.  

I believe Beretta recently dropped the MSRP to $39.00 but MGW has them for $34.95 all day long (as does Beretta if you buy more than one at a time).  Better than that is Beretta frequently puts these things on sale.  The last batch I bought had a combined 65% discount with free shipping.  You know what else goes on sale?  Mecgar 18 round magazines.  A few years ago I got 10 for 19.95 each plus a flat $4.50 for shipping.  I placed a WTT ad on the Beretta forum, offering to trade my new 18 round Mecgar mags for like condition Beretta PVD mags.  All 10 were spoken for in less than 24 hours.  I now have 20 of the PVD mags (for 2 pistols) and my average price per mag is under $25.00 and that include the cost of shipping.  

I have the PVD and standard black Beretta mags you speak of and they both work well.  Having said that I personally can't justify paying the extra coin for the PVD/sand resistant coated mags.  FWIW I also use Checkmate mags.  I had an issue with (2) Checkmate mags a few years ago failing to lock the slide back when empty however, I returned them to where I purchased them and have since purchased additional Checkmate mags and they work well.  I hope this helps.

This is what all three of the brand new 17rd mags did in my new 92a1. The edge of the followers would hand up on the slide lock.  2 months later i received three new mags from Beretta but dont like or trust them to use them. I found the 17 rnd mags had a follower that is hollowed out and thin in construction to allow the 2 extra rounds.
Fuck that !  i went with the proven 15 round, I buy the sand resistant mags and recently bought a bunch of new GI mags with the aluminum bases.

Since I posted I've cracked the basepad on an OEM 17 round Beretta magazine.  So if you want something with more capacity than the OEM 15 rounders, I'd go right to the 18 round Mec-Gars.