A short disclaimer first.
1. I'm aware of the fact that a computer's onboard line input is perhaps the worst option for sound recording.
2. I also know, that a player's HP out is for headphones, not for high-resistance load. To measure and analyse audio output an oscilloscope should be connected to actual headphones or a simulated reactive load with impedance of real cans.
3. In my experience any graph, especially a Headroom FR chart is misleading and can't tell you anything about any audio gear.
Therefore what I did can not be regarded as an accurate experiment. Some may remember the infamous "iPod bass roloff" hype which led to flame wars across many a board on the web, including this one, a couple of years back. The guy who started it simply hooked an ADC to iPod's HP out and got a terrible (and predictable) FR curve.
This said, I, however, do believe that waveforms of different shapes produce different sounds.
I took an iPhone 3G 3.0 and a kid's iTouch 2G 2.2.1 and recorded the playback of one ALAC file (happened to be The Beatles' Help, but could be any) using Mac Pro line in and Audacity. The volume was set to max on both devices. The iPhone's output turned to be louder so I butchered both sequences with Normalize command. Here is a fragment of Audacity waveform analyzer:
iPhone 3.0 on top, iPod Touch 2.2.1 on the bottom. The more complex waveform of the upper graph means more higher harmonics, which leads to better timbre rendition.
Edit: I aligned both waveforms to a millisecond and reposted the image
Sorry for long post.