UPDATE (11/Oct/2012): the latest BUZZ Player and Good/PowerPlayer updates removed AC-3(A52), E-AC-3 and TrueHD(MLP). The developers of GoodPlayer stated (link) the patent holder asked for quite a lot money for the license. I've asked the developers whether the decoder(s) could be provided as optional In-App Purchases. HustMobile answered it might be possible.
Unfortunately, as the BUZZ Player folks have also explained, removing AC-3 support also means it'll no longer play AC-3 MKV's - one of the strongest features of the player.
Here's the update list, along with some other players:
UPDATE (some hours later): in my just-published article, I've also offered an alternative to the problem of dropped AC-3 support: automatically and easily adding AAC audio tracks to your AC-3 only multimedia files. It's the best way to go if you don't want to manually restore the still AC-3-capable versions of your third-party media players and don't mind some manual video conversion.
It seems all iOS developers with a multimedia player supporting AC-3 (Dolby Digital) audio playback are forced to remove the support, as has also been announced by the developers of GoodPlayer (dedicated announcement).
The first (known) victim of this is exPlayer HD, of which the no-AC3 version has just hit the AppStore:
(click for original image. See the annotation, a red rectangle, which announces the changes.)
This means you no longer will hear anything when playing back THIS (MKV) or THIS (MP4), AC-3-only file. (Note that the latter is iOS-native, which means you won't hear anything even without updating if you play it back using the hardware decoder. For example, in exPlayer HD, if you answer “Yes” to the question “The movie might be played by iPad player, do you want to use iPod player to get better playback performance?”, you won't hear anything – as opposed to the case of answering No.)
Note that, as has been already hinted on in the sentence before the image, exPlayer HD is the first known player to have already removed the support. As Dolby? Apple? seems to force every iOS developer to drop AC-3 support, the other players will surely follow. It's, however, not guaranteed the update notes will at least mention this, let alone the developers actively warning their customers (as did GoodPlayer's HustMobile folks) and explaining to them how to back up and, when needed, restore the still-working version.
What can you do?
If you don't need the probably small (or non-existing) other changes / improvements in the affected players, you simply need to follow the advice of the GoodPlayer folks – or, for that matter, any “Back up your IPA files in your iTunes before updating” tutorials around the Web. Then, even if you click / tap “Update all” on your desktop iTunes / iOS AppStore app, you can easily restore the old version any time.
This, however, needs to be done manually as Apple's AppStore in no way has any support for selecting a previous version for installing. Which would be very important to, say, users of no-longer-updated iDevices. The desktop iTunes happily downloads the new versions of apps no longer installable to first- or second-generation iPhones / iPod touches (maximal iOS version: 3.1.3 and 4.2.1, respectively). You only need to delete the app from your iDevice once and try to reinstall it to be completely shot: you no longer can use the app you've paid for as it is simply incompatible with your device and, unless you've backed up the older versions of the app, you in no way can (legally) acquire them, through iTunes / AppStore / Apple. This has resulted in a lot of angry discussion threads – see for example THIS highly recommended one.
I recommend THIS and THIS article, also linked to from the GoodPlayer developers' warning, on backing up and restoring current / old versions.