On my new bike, I noticed that while in the smallest front ring (triple), and some of the lower gears, while going up a hill, the chain would seem to skip a tooth randomly, sending the cranks forward a slight jump.

There was no pattern to it, nor was I able to get the bike to do this in either of the bigger chainrings, even while standing up and cranking.

What would cause this? I am assuming this is not chain stretch...

My guess is that it would have something to do with your chainline. My chain will skip as well if i put it in my smallest front cog and my smallest back cog. The idea to avoid it is to keep your chain in a straight line. Search chainline or go to parktools.com. Im pretty sure they have a page on chainline which could help you out.

Your problem is unlikey the chainline. Have you installed a new chain recently? A new chain on worn cogs often reveals one or two worn cogs. If I understand your post, you have skipin the little ring and some of the largest cogs? That's what I had when I changed to a new chain after 6000 miles. The chain wasn't close to the allowable 1/16" per foot elongation. A new cassette will cure the problem.

You should monitor chain elongation and change the chain before it reaches 1/16" per foot. Even this change interval will not guarantee that some cogs won't be worn at the first change of the chain. To increase cog life, consider alternating the use of two chains, about every 1000 miles. With this technique, you'll never put a new chain on worn cogs and the chain of chain skip is greatly reduced.

I've recently reinstalled my worn cassette, with a half-used chain and it's working fine. I'll get a lot more miles from this cassette now.

This bike is new... this was occurring on one of the first rides, the bike has less than 50 miles on it (to the best of my knowledge anyhow, its new from the LBS).

This happened on the smallest front ring, maybe 3rd gear on the back.. not a very big stretch as far as the diagonal stress on the chain would go. Weird.

The bike will go back to where it was purchased for some different components this week anyhow.. they can deal w/ it :)

The problem is more likely the need for an adjustment of the shift cable tension, although a defective cog is certainly possible. Your LBS should take care of it for you.

Could be as simple as a rear derailleur adjustment. Your shop should be able to sort it out.

1. rear deraillur adjustment.
2. barrell adjuster.
3. cassette locking ring not tightend down sufficiently.
4. cassette/free hub spacer required.
5. wheel flexing laterally under torque. (does it only happen with you on the bike, or on the stand too?)

A strong possibility is a misalignment of the rear derailleur hanger. As you shift between front and rear sprockets, the angle of the derailleur cage changes (as it must, to take up the excess chain slack). If the hanger is bent, the alignment of the pulleys with respect to the sprockets can change as the cage angle changes. I have seen several cases where a derailleur hanger is bent such that when the derailleur is adjusted for the largest chainring, it will be out of alignment for the smallest chainring (and vice-versa).

A hanger becoming bent in the way that causes this problem is actually more common for new bikes than for bikes in use. Typically, the rear derailleur hangs nearly vertically below the wheel, and if the derailleur takes a hard knock, it causes the hanger to bend inward on a horizontal axis (i.e. it swings in and up). But when a new bikes is being shipped in a box, typically the rear wheel is not installed and the derailleur B spring pulls the derailleur back so it hanges to the rear of the drop out (and indeed is the rearmost portion of the bike as it sits in the box). If the shipping box takes a good strong whack at the back, the hanger can be bent on vertical axis (i.e. twisted inward on a vertical axis). This type of bend can produce the type of problem you describe - where the derailleur alignment (and indexing) seems to vary inward or outward, depending on which chainring is used.