I have a 2006 LHT, and for the most part think that it's been a fantastic bicycle. My reservations have mostly to do with a shift in my needs and desires for a bike since I purchased it, though I do have one problem with the design: as others have said, fitting fenders can be a problem. In my case it's not a matter of matching them to the tire size, it's that big wide fenders are difficult to get low enough to not interfere with the straddle wire of some cantilever brakes. I ended up sawing off the front of the fender, which is irritating, but at least I can use the front brake. I haven't had the energy or interest in spending the money to develop a better fix. Luckily, spray off the front wheel isn't such a big problem, but it can be annoying on rainy days.
Other than that, my issues are more about change in pace. When I bought the bike, I was still very much interested in serious touring. I haven't let go of that idea, but it's on long-term hold for the moment for a number of reasons. The LHT is at its best when touring on the road, commuting in rough conditions, hauling serious loads or zipping along non-technical paths. I don't have much need for any of those uses right now, so I mostly use it as a commuter. Given that I don't typically need to carry much, that I often have a fairly large amount of riding to do as commuting goes and that the roads are pretty good, it's a bit of overkill to use it for getting around right now. It was better when I lived in the center of town. It's also currently my only bike with fenders, yet isn't well-suited for road riding in the rain - the position is quite a bit different, the pedals are flat without clips, and the bike is generally just a tank. There's no motivation to ride fast on this bike, and I like it just fine that way. So I'm not having loads of fun with my LHT right now.
But! Put the LHT in its element and it becomes an amazing ride. It's stable even when loaded to the gills, it floats along dirt roads and paths, it inspires confidence on long downhill stretches of crappy pavement. Even when it's not the bike I turn to when I want to have fun, it continues to be useful in ways that my road and mountain bikes can't remotely approach.
If I get into the grad program I want, or end up with a reasonably good-paying job, one possibility I'm thinking about is building up a Pacer with a triple, downtube shifters and fenders for lightly-loaded commuting, long-distance riding and winter road riding and training. With that done, I would feel good about switching the LHT to risers and v-brakes and generally focusing it as a bike for Serious Business. That's what it was built for; that's what it does best. Absolutely amazing machine. The fact that I'm thinking about a second Surly should tell you all you need to know about my opinion of them: solid, well-designed, affordable, versatile. Good bikes.