Pretty sure that changed a long time ago. Auto's are now generally preferred for off road use, especially the big rock crawling buggies. Transmission coolers are cheap and modern electronic auto transmissions are as reliable as anything else made today (which is pretty darn reliable.)
I'm a stick shift guy too (my DD 2wd Mazda pickup is a manual and so is my wife's YJ) but we're all going to have to accept that the day of the MT will soon be over.
Toyota dropped the MT from the 4runner way back in 2001, the FJC and Xterra have been dropped from their respective lineups. Full size 1/2 ton trucks haven't had MT's for a decade or so and for SUVs it's even worse - I think the last Suburban to have a manual was the old "square" body style that ended in 1991. Expedition, Tahoe, Sequoia, R51 Pathfinder (the 2005 - 2011 models) and Armada have never been sold in the US with manual transmissions.
The only way to get a 4x4 with a stick shift nowadays is either to go with a Jeep Wrangler or a Tacoma/Frontier (even the new Chevy Colorado/GMC Canyon is automatic only.) I suppose there's a slight possibility that IF Ford reintroduces the Ranger to the US market (there's been scuttlebutt about that) it might have a manual but I wouldn't bet on the truck even showing up in US markets - it would take sales away from the F150 and with cheap gas there's no incentive to build any more mid sized or compact trucks.
The only exception to the above I can think of is 3/4 - 1 ton and up 4x4 trucks from Ford and Dodge
might be available with MTs. I don't really know.
EDITED TO ADD: I just remembered there were some models of the Jeep Liberty that were sold with MTs (6 speed I think.) I don't know how rare they are though, but they are a true body-on-frame SUV with a low range T-case. The first generation "Round eye" Libertys were a little - how can I say this? - "Girly looking" but the later ones looked OK. Not sure why Jeep dropped the Liberty, I always thought it was kind of a nice sized compact SUV. A few years back the wife and I rented a 2wd Dodge Nitro (same thing as the Liberty) and that thing was a
tank. Solid as a rock.
Now they've replaced it with that "Cherokee" AWD crossover. Just what we needed, another crossover.
