Not sure that it ultimately matters, but I recently purchased an E2160 proc and the stock cooler is of the aluminum variety.  That's not surprising.  What I found somewhat strange, however, was the changes in design when compared to the last aluminum stock cooler that was packaged with an E2140 that I purchased last fall.  It's hard to describe, but it seems to be a lower profile.  The second thing I noticed was the surface that contacts the proc heat speader is a much larger surface overall.  In other words, it is not like the other stock intel coolers I've seen where the base of the cooler is sort of terraced to create a platform that contacts the proc.  This new one just has a large surface with a circular machined area the size of the circular base of the old style.  Also, the machining on the base seems to be of much lesser quality.
 
I hope this makes sense.  Like I said, I'm not sure it matters in the end, but I am certainly curious what others think about this.
 

From what I've seen, there are three versions of the stock Intel fan going around now.  
 
The first is the full height version that comes with the 65nm Core 2 Duo and Quad CPUs. It has a copper base. I ended up with these when i bought my E6300 in 2006.
 
The second is simply an all aluminum version of the first fan. I ended up with one of those when I bought an E2140.  
 
There's a new version as you described. It's not nearly as tall. Presumably they can use the cheaper, smaller, fans because the 45nm and lower clocked 65nm processors don't put out much heat.

I haven't even used my stock HS for my E4400:
 

 
If you could post a pic of it, perhaps you could compare and point out the differents on the contact side.

I know exactly what you are talking about and Mandrake is correct...
 
There are three different types... When i got my e6300, e6600 and q6600 they all came with the copper full height... Got a e2140 for my dad HTPC and got all aluminum... then got a e2180 for my grandmother and it has the half height one. Nothing to worry about here at all, temps are still fine all round

Thanks people.  I prolly should've posted a pic, but I think Mandrake made me realize something.  Perhaps the smaller cooler is provided with the the latest steppings.  I've got an E6600 B2 stepping that came with a copper cooler like the one in Grimmy's photo, an E2140 L2 stepping that came with an all-aluminum cooler of the same design as the copper one, and an E2160 M0 stepping that has the all-aluminum low profile one.  I beleive that the Tcase max is higher for the M0 stepping, meaning it can get away with a lesser cooler.  I believe that would also explain the use of this cooler with 45nm procs as well which I think just produce less heat.
 
Anyhoo, I found it interesting and was not aware of this third cooler variety.  Thanks again for respondign to such mindlessness.

My e2160 M0 stepping came with the full-height aluminum cooler (purchased in January).

hmmmmm......I guess that shoots my theory down.  So, is appears that Intel is now skimping on their hsf's.

I got a 2140 about 5 months ago, and then a 2160 last week.  Heat sinks and fan are the same size, but the numbers and such on the fan don't match.  I put the 2160 in my rig, and will use the first fan in case there was a negative change in it's design, though.  I overclocked the 2140 to 333 fsb (2.66), and will hope to do the same fsb with the 2160 (3.0 ghz) and give the 2140 to my folks for their computer.  
 
Out of curiosity, how much can I expect temps to go down if I were to go with a Arctic Cooling Freezer pro on one of these?  Summer isn't too far away....

p3matty--I've done about the same thing as you.  I built a machine for my wife with the 2140 using the copper base stock cooler that came with the 6600 for my rig.   I had it oc'ed to 333 fsb and temps were around 38c idle and 58c~60c load with prime95.  I never actually used the aluminum cooler of the same design that came with the 2140 to see the difference, but I think I've read that you could expect few degrees higher.  Overall, the stock copper hsf seemed quite acceptable as a cooling solution for that setup.  I decided to donate that machine to a local charity and build a new machine for my wife using a 2160.  This is where my confusion came in because the cooler that came with the 2160 is of this new, mysterious variety.  It really doesn't matter because I had already decided to use an Arctic Cooling Freezer Pro on this new build.  I just got it put together over the last couple of evenings and haven't installed windows or anything yet, but I'm curious about the temps as well.  Even though I'm using a 2160 rather than the 2140, it should give me an indication of the difference between the stock hsf and the Freezer Pro.

No worries, I'm doing the same.  I see that Newegg stopped charging shipping on an ACF7, so I ordered one today.  Like I said, though, the two coolers that came with my 2140 (5 months ago), and the one I got yesterday with the 2160 looked the same.  I had the 2140 on a fsb of 333, which gave me 2.66 ghz.  I'm worried about taking the 2160 there without the ACF7, though.  I'm going to see if I can boot it up at 333 and stress test it a bit and get some temp readings, and then do it again once the larger cooler arrives.  
 
Also after reading on the Arctic Silver website, I put that one the chip improperly, so I'll have to at least redo that!

I haven't oc'ed the 2160 yet, but I would think that 333 fsb should be no prob even with the stock cooler.  
The ACF7 should provide a little additional headroom, though.