I have used a lot of different tools putting together the laser cut buildings that make up my Old West town of Calamity. First, I would like to emphasize that you don't need fancy tools to put these buildings together, some large rubber bands will do the job. Model railroad laser cut kits tend to be more complex and tools definitely help get those together. In general tools make some things easier, especially when it feels like you need four hands to get something together. If you like to scratch build your own structures some of these are downright invaluable. If you see a stock number, that's the stock number for that item from Micro-Mark
First up are the spring clamps. I have a bunch of spring clamps in a variety of sizes. I'm showing the two smallest clamps I have and the ones I use the most often. The small multi-colored clamps came from Micro-Mark. I bought the bucket of 50 (stock #82979) and there have been times when 50 hasn't been enough. The rest of my clamps I picked up at Home Depot can came in a nylon bag for like $7 (NIL 22-Piece Spring Clamps). There were 4 different sizes of clamps in the bag, the very largest I rarely use (at least for hobby use) but the other three sizes I use all the time. The smallest is the same size as the ones I bought from Micro-Mark and are a bit stronger. My own philosophy you can never have to many clamps.
The next clamp that I use quite frequently is the "right" clamp. This is used to clamp two pieces together that are at right angles to each other. The pair I have are probably close to 30 years old at this point and I have no idea who made them. Although I use these frequently they aren't particularly good clamps. There are better ones out on the market and I'm considering replacing the pair I have with something newer.
The clamp I really like, although it can be a bit fiddly, is the mini 4 corner clamp (#60716). It will go from 1/2" x 1/2" up to 4" x 5". Basically it wraps around a cube or rectangular building to pull the corners in tight and square for gluing. Its not possible to use this clamp in every situation but I use it whenever I can. Quite frankly though some rubber bands would do the same job just not as well since the rubber bands can't hold your object square.
While I'm talking about keeping things square here are some neat little 90 degree angle plates (#60713) that I picked up recently. These are 1"x1"x1" and I use them to keep parts vertical while glue sets. This is the smallest size that I could find.
The other way to keep larger items square while they dry is the magnetic jig (#60304). This consists of a steel tray with the edges turned up at 90 degrees. Then you use the magnets that are sandwiched between the plates to keep everything tight and square while the glue dries. These are powerful little magnets and it takes some effort to move them. I picked up the extra set of 8 magnets (#60305) and I'm quite glad I did, they have come in handy.
My last handy tool helps me keep things square and can be used to help weigh things down. These are 1-2-3 Precision blocks. I have an economy version which was just the blocks (#84644) and an ultra precision set that came with a case, screws and an allen wrench (I got these from Shars Tools). Apparently these are used to gauge things in some type of machining process. I use them to hold things in place (they weigh about 1 pound each), and since they are machined at precise 90 degree angles they can be used to hold things square as well.
Beyond that I use the regular assortment of modeling tools; x-acto knives, razor saws, pin vice and files. I prefer Titebond Carpenters glue for the laser cut mdf and plywood kits. Super glue is not a good choice as the surfaces are so porous. Regular white glue or PVA will work just fine as well. And remember if you don't have these tools all of the laser cut mdf and plywood buildings will go together fine using just a few rubber bands to hold things together while the glue dries.