It might be just me, but holding the 3DS in air (Not resting my hand on anything.) just seems uncomfortable. Maybe i'm just so used to normal controllers but it's seems like it's to thin and the circle pad is kinda cramped.. I dunno. On the DS I used the bottom middle part of my thumb to use the d-pad, whereas with the 3DS I can't really do that with the circle pad and I have to move my left hand that I'm holding it with to put my whole thumb on the circle pad, that ends up kinda cramping my hand after a while.
It's kinda hard to explain, I'm thinking of getting the circle pad pro just to see if it feels more comfortable even whole playing games that don't use it.

How do you guys hold it without being comfortable?

-.- what is this?

Normally, to make it comfortable, I hold it in my feet.

Though my disco stick works as a great stand for my unit.

I sort of balance it on my pinkies, use ring fingers on the L/R buttons, and I got two thumbs and four fingers left in changing positions depending on the game.

I'm a lady with pretty tiny hands so I hold it with my thumbs on the face buttons and the slider, index fingers for the shoulder buttons.

Now here's where it gets a bit strange. On my left hand I have the 3DS resting on my pinky with my other two fingers on the back.

On my right hand I have the 3DS resting on my ring finger with my middle finger on the back and my pinky just doing whatever it does.

EDIT: Ah, I forgot that I hold it completely differently when I'm drawing. My left hand ends up more like my right hand normally is. But I draw right-handed so I'm holding my stylus like a pencil and I have the top part between my ring finger and my pinky. You can imagine the grooves I get when I've been on a drawing spree. XD

EDIT2: Wait a minute, I just re-read the question. It's asking how I hold it and be uncomfortable. What an odd thing to ask... I dunno, maybe like how I always do but with a leg or foot asleep.

In my hands. Hur Dur.
I tend to rest it on my lap whilst playing some games like The Rolling Western, but mostly I just hold it in the air.

Mostly i'm playing it in bed. So when i play games where i constantly have to use the touchpen i rest the system on my baby finger a little. Never had any problems during Uprising sessions so i guess it must be kinda comfy.

Well if you find it uncomfortable, maybe a 3DS XL will suit you better...

I curl my middle finger, ring finger, and pinky finger inward toward my palm. The 3DS rests on those. Then, my index fingers on my hands work the shoulder buttons. I arch my fingers to do this successfully. My thumbs are then left to use the Circle Pad, +Control Pad, and face buttons.

with my hands.......................................

I hold my over the fire place, to watch it burn.

Hold it with my mouth and use my left eye to control the slider and a right earlobe works wonders pressing buttons... Very comfortable

My cat holds it while i hold the cat

I hold it so the corners rest on my palms. When using the touchscreen I hold it in my left hand with my pinky supporting the bottom, for games like Kid Icarus: Uprising I often rest it against my knee.

You never really think about these things until someone asks.

Stylus in the left hand, holdin' the unit with mah right........

I hold mine the same way, I'm pretty sure. My hands are small, and I think that helps me hold it, too.

Thread Win.

I hold put my thumbs on the Circle Pad with my middle fingers under each side from my joints to my fingertips. My palms hold the sides loosely. My pointer finger comes to the shoulder button at the joint making it quick and comfortable to push them with hardly any movement. One end of my stylus always rests between my thumb and pointer and the other end (the head) between my pinky and ring finger.

Years of Game Boys and DSs have reshaped my middle fingers, they are slightly bent to hold them better D:

-Back of the console rests on middle-to-pinky fingers, of both or only one hand (depends on the use of the touch screen).
-Index fingers for the R/L buttons
-Thumbs are for buttons/dpad/opad/fast touchscreen input.

If it uses the book style, then I hold it like a book, duh.