2nd Attempt (somewhat comedic attempt):
My prefix describes some folks you might know,
who shun convention wherever they go.
They're not rebellious, they don't break the rules,
but you might find them ... strange in the things that they choose.
If you know who they are, then know they aren't I
For I am a different kind of guy
This sounds like someone who is Queer (please don't stone me, I'm not trying to be offensive).
For infix the first, I have a bad habit
I am guilty myself, I have to admit.
For this awkward thing manifests when I speak,
And for many more too, especially the meek.
This sounds like someone who mumbles. queer-mumble?
Next infix is easy, you're doing it now,
You don't think about it, but you do it, somehow.
Take that and swap height with width, you are almost done,
Infix 2 is now complete, and the suffix has begun.
I'm pretty sure this is referring to seeing something, or C. When you swap the width for the height, you are left with the letter U. so queer-mumble-u.
The puzzle's almost over, this is your destiny
Just take the apple and throw it out, and closer you will be.
Take what's left, chop it up, and give it to The Pope,
If you have his help, there is still some hope.
Maybe I was taking this the wrong way last time. When you throw out Apple computers, you are left with windows! So let's chop it up, give it to the pope, who provides for the meek and weary, and we are left with widow. So Queer-mumble-u-widow.
The answer is of course,
quemumbleuwidow, which we all know means to be left baffled by a made-up word.
I believe the answer is
Emotionalism, though I can't figure out what the second infix and suffix have to do with this.
My prefix describes some folks you might know,
who shun convention wherever they go.
They're not rebellious, they don't break the rules,
but you might find them ... strange in the things that they choose.
If you know who they are, then know they aren't I
For I am a different kind of guy
This sounds like someone who is emo.
For infix the first, I have a bad habit
I am guilty myself, I have to admit.
For this awkward thing manifests when I speak,
And for many more too, especially the meek.
This sounds like pacing. So we have emo-motion. emotion?
Next infix is easy, you're doing it now,
You don't think about it, but you do it, somehow.
Take that and swap height with width, you are almost done,
Infix 2 is now complete, and the suffix has begun.
I'm pretty sure this is referring to breathing, so maybe breath? emotion-breath.
The puzzle's almost over, this is your destiny
Just take the apple and throw it out, and closer you will be.
Take what's left, chop it up, and give it to The Pope,
If you have his help, there is still some hope.
If you throw out the apple, you'd be left with the seeds? Pope and seeds, poppyseed? So we have emotion-breath-poppyseed. That can't be right. How about emotionalism?
I believe the answer is
Emotionalism, though I can't figure out what the second infix and suffix have to do with this.