Here is a spreadsheet comparing the geometries of both bikes next to one another in corresponding sizes.
The obvious difference between these two frames is that the Salsa frame is made of aluminum, while the Surly is steel. This is the point at which people start to be divided into two camps. A lot of folks will choose the Mukluk for some weight savings and corrosion resistance. Others will prefer the Surly for the springy ride quality and small tube aesthetics. For their intended uses, and considering that common tire pressures run from 8-14 psi, I don't know that the Mukluk will ride as harsh as a traditional MTB frame. As to corrosion and the Surly, a healthy dose of Frame Saver will pretty much take care of that. People have been riding steel bikes in adverse conditions for almost 100 years, it's pretty much a non issue with proper maintenance.
Both of these bikes use steel forks. This is a good point to start delving further into design, as the bikes differ wildly up front. The Surly uses a fork designed to use a 135mm rear spaced hub dished to a 17.5mm offset. This is to allow people to use two identical wheels front and rear. A common practice is to run a geared hub in the rear, with a SS front hub and bail out freewheel up front. This provides you a back up drive train option if either the rear free hub, or something such as a derailleur were to fail. The Surly fork is not suspension corrected. This means you can run a suspension fork in the bike, but it will have the effect of slackening the angles, as well as raising the bottom bracket. The Surly fork has front rack mounts and fender eyelets. For 2011 Surly dropped the cantilever brake bosses from frames and completes. The photo below is an aftermarket Pug fork. It still comes with canti brake mounts.
The Mukluk frameset includes Salsa's Enabler fork. This is a suspension corrected rigid fork designed to also use a 135mm rear SS hub. It differs from the Surly in that it is made of slightly lighter tubing and uses stainless steel dropouts. It also has rack mounts, two Everything Cage mounts (for bottle cages as well,) and has front and rear positioned fender mounts. Although it uses the same 135mm hub as the Surly, it is not offset. This means you can build a dishless, even tension wheel. It also make the wheels on a Mukluk front and rear specific, you cannot switch them if something goes wrong. The longer length means that you can swap the fork out for any common 29er suspension fork without altering frame geometry.
Working backward from the fork the next obvious points to talk about center on front end geometry. In general, the Salsa is quite a bit taller at the front as compared to the Puglsey. The head tube length per size is nearly an inch longer from the Salsa to the Surly. Combined with the longer Enabler fork the Salsa will be about 2"s taller at the top of the head tube compared to the Surly. The easily seen effect of this is that fewer spacers will be needed if you like your handlebars higher relative to your saddle. Conversely, if you like shorter front ends you may not be able to get the handlebar drop you prefer on the Mukluk.
Front end steering geometry is slightly different between the two bikes. The head tube angle is slightly slacker on the Mukluk, while the fork rake is slightly higher. The Surly has a slightly steeper head angle and less fork rake. From bike to bike the two front ends should feel pretty similar, with the Salsa front end being slight further away from the center of gravity. The Puglsey leans a bit more traditional mtb up front, with the Salsa going slightly more touring-esque.
The effective top tube lengths vary between these two bike a fair bit. The Pugsley runs shorter by about a 1/4" as compared to their Karate Monkey 29er. The Mukluk is just a hair shorter than the El Mariachi 29ers. In general, with either company you would ride the same sized frame as you are riding now. So if you like a 18" Karate Monkey, you would likely fit a 18" Pugsley. If you ride a large El Mariachi, you'd probably be at home on a large Mukluk. Personal preferance comes in to play here as well. Most folks prefer a slightly shorter top tube for a more upright position on a snow bike. Both of these bikes largely help with that right out of the box. Still, some people prefer to drop down a size on a snow bike.
The seat tube angles vary between the two bikes by a full degree. The Surly runs at 72 degrees across the line, with the Salsa coming in at 73 deg and 73.5 deg on the XS. The Surly runs the slacker seat tube to move weight over the rear wheel. The Salsa has other features that shift weight back. Personally I prefer a 73 deg seat tube, but my Fargo is awfully nice at 72 degrees.
The chain stay length and drop out configuration differ on these two bikes. The Pugsley uses horizontal dropouts to allow for a an adjustable chain stay length and to allow for easy single speed chain tension adjustment. The stays in their shortest position are a bit shorter on the Pug. They measure almost half an inch shorter than the Mukluk. Some folks like to run Monkey Nuts on their Pugs to make the rear end a bit longer and the ride a hair more stable. With Money Nuts installed the two bikes would measure nearly the same. The Mukluk cannot be run as a single speed without a tensioner of some sort. The dropouts on the Mukluk are traditional vertical dropouts. Mukluks use special 170mm rear dropout spacing with no offset. This ends up being the same 17.5mm offset for the drive train, but moves the non drive side over just the same. This means you have to buy a specific hub, but that wheel will build up with no dish and will have near perfect spoke tension. The Mukluk also comes standard with a machined alloy adapter that will allow the use of traditional rear 135mm hubs. You would build the adapter wheel just as you would a Pug rear wheel. The Surly uses the same 17.5mm drive side offset and 135mm standard rear hubs.
Wheels. Here are where the bikes are quite different. The Mukluk uses non offset wheels front and rear. It is set up to use a 170mm dish less wheel in the rear and a 135mm dish less wheel in the front. They are not interchangeable. Even if you use the available 135mm rear adapter, the 135mm rear wheel will not be interchangeable with the 135mm front as the wheel's dish will be wildly different. The Pugsley uses interchangeable 135mm dished wheels front and rear. 29er wheels can be built for use in either bike. The Pugsley is more limiting in this regard, as you need to use offset rims to end up with decent spoke tension. The Mukluk can use 29er wheels as well, although they still have to be built specifically for the bike. A typical rear SS 29er wheel can be used as front Mukluk wheel with no modification in the Enabler fork, but could not then be used in a 29er suspension fork.
Drive trains can be set up much the same on both bikes. They both use 100 mm bottom bracket shells. Both bikes use full cable housing for all brakes and derailleurs. Both bikes use specific front derailleurs. The Mukluk uses a direct mount front der, the Pug uses a bottom bracket mounted E type derailleur. If you want to run an internal hub, (ie a Rohloff or Shimano Alfine,) you have to use a Puglsey. The Mukluk is not designed to work with any existing internal hub. There may be a way to make one work, but Salsa did not design that into the Mukluk, and would likely not support any mistake incurred by using one.
Stand over height has been reduced on the Pugsley in 2010-2011 models. They now feature a braced seat tube that lowers stand over height down to acceptable levels for the respective frame size. Surly bikes have long been criticized for being "tall" in the stand over department, so this is a great change over past models. Even with the taller front end, the Mukluk still beats the Surly in stand over height in ever size by at least 1/2".
A noticeable addition to the Mukluk line up is the addition of an XS size. This bike is quite a bit smaller than the smallest Pugsley previously offered. The stand over height on this size is in just north of 26"s, making it shorter than some small 29ers. With few exceptions, this is the first true XS snow bike that has been offered. We already have some customers excited about this bike, as it will allow them to comfortably fit a fat bike for the first time.
So there you have it, a general rundown of both bikes. There are some distinct differences that will likely push consumers one way or another. Either way these bikes are about the coolest way you can roll this winter. Let me know if you have any other specific questions and I will address them as I get them. Happy Friday all.