Without doubt platform-dependent mobile apps: by nature patents expire.
Having said that, the silliness of patented codecs seems to have been recognized for lower bitrate use cases (image, speech, audio) so I guess it's only a matter of time for video.
I think a Googly approach where the encoder and decoders are assumed to be software like anything else in Chrome and updated every 6 weeks would be interesting to see.
There are multiple reasons for this, like the huge cost of re-encoding everything that was once encoded in MP3, the broad hardware and software support or the fact that MP3 is good enough for most purposes.
Broadband plays a role here as I'd bet that if it weren't so prevalent today, then people would actually want formats that sound better at lower bitrates. As it is, Amazon doesn't have a problem in selling songs encoded at 256 kbps, although you won't hear a difference when comparing that to an 128 kbps encoded AAC file from iTunes.
An upgrade scheme only works if files encoded with the newer codecs don't have a problem being played on older software/hardware, because here's the thing ... H.264 is already good enough as far as video codecs go, just as MP3. And this is doable, but the newer patents will most likely touch the encoders, not decoders and the newer patents themselves will get more fragile over time, as you can't really innovate on top of the same technique forever.
All in all I agree with the general sentiment ... proprietary platforms are more dangerous than patents and native apps are more dangerous to the future of the Internet than proprietary codecs.
You could even argue that the fact that it always comes with such (relatively) large size video files makes the improvements of AAC over MP3 even less relevant, but still the "standard" has moved on and everyone needs to keep up. I also believe that 3G phones needed to support AAC but I could be just making that up.
I've seen one "mp3 player" that dropped AAC support, but I can't see that happening for any device that also wants video. The direct result will be paying separate royalties on two mostly overlapping audio formats.