I have the GAP Long and Lean jeans and the Really Skinny pants (not the jeans) - both stretch out a bit, but not enough where the 'muffin top factor' (and avoidance thereof) would come into play.
As others have said, I really think the rise of the pants/jeans is the main thing when it comes to avoiding the so-called "muffin top." I used to think that such pants were too small or that my own body shape just wasn't meant for certain styles, but in the end - it really does come down to the rise.
In terms of something 'close to skinnies' - the Kut from the Kloth skinny jeans (not a true skinny, but close enough!) work well for me, and I think this is because the rise is a little bit higher than some other skinny jeans I've tried. Just for the record, I've experienced "muffin top" with jeans that are the exact same size as other jeans I've tried where I didn't have this problem at all - and this is even within the same brand.
I'm 100% convinced it's all a matter of rise when it comes to avoiding this problem. Sizing up or down might not help at all, if the rise just happens to hit you in the wrong place. Come to think of it - I've tried on pants and jeans that were clearly too big for me, and I *still* saw the dreaded 'muffin top'.
I recommend going and trying on a whole bunch of jeans in different brands and styles and getting to know which brands/styles do not have this effect on you.
In the meantime, try the GAP Really Skinny pants - these worked well for me last fall and winter, and no muffin top to speak of, and I was able to tuck them into all kinds of boots and so on.
Yes, jeans stretch out - but the thing is, if there's too much of the muffin-top/roll-age thing going on to begin with, all that will happen is that there'll be a slightly smaller 'muffin top' happening once the jeans stretch out a bit.
What I'm trying to say is that the cause of this problem is where the jeans hit you in the mid-section, and this has a lot more to do with the rise than the size. I have sized up in jeans/pants, thinking that this would correct the problem, and ...no, it didn't really work. I ended up with baggy pants *and* a muffin top.
It's the rise, not the size.