There are three very important factors that go into determining boot comfort:
1. The last. A “last” is a form used to mold a boot foot. (See the boot terms tutoral I wrote for HotBoots here. Some lasts accommodate feet well, allowing the bootmaker to form the leather of the foot in a way that provides adequate room for the foot, but not so much room that the foot slides around.
Better lasts are used by quality manufacturers, such as in the U.S., Lucchese, Dan Post, Champion Attitude, Paul Bond, as well as many of the high-end, hand-crafted bootmakers, and several other commercial bootmakers. Cheap lasts are used in boots now made in China, such as Frye, Harley-Davidson (brand of boots), and a few others. Always check to see where a boot is made. R.M. Williams in Australia makes an outstanding boot. Boots made in Mexico vary, but are also usually made well.
2. The sole and insole. This is what your foot rests on while walking. The better the sole, the more comfortable the boots are. Really good soles may be made of leather or, sometimes, synthetic materials. A good sole will mold to a person's individual foot. All feet are different, so the molding process is what makes a boot comfortable for the long-term, while it may feel uncomfortable at first during the break-in period. The sole is built right into the boot and sewn in place. A good boot manufacturer will also add an insole, which is a small cushion that rests on top of the sole and with which your foot has direct contact. You can buy additional insoles, as well, at a local store.
The most important thing to keep in mind is that if the boot's sole does not conform to the person's foot, such as for bumps, arches, bones, etc., then the boot will never be comfortable even with a good insole.
3. Sole construction, such as with the use of pegging, and a full or 3/4 shank in the midsole, is also very important. A sole that is attached with pegs is more durable and flexible than a sole that is stitched on to the foot. A sole that is glued is less flexible and thus less comfortable. The better boot makers still use pegs to attach the sole (look for “full pegged sole” or words to that effect.) Or, simply turn the boot over and look at the sole. If you see small round 3 - 5mm dots, then you have a pegged sole. If you see stitches from threads, then it's stitched. If you see neither, then it is glued.
Also look for information on the boot description or tag that indicates what type, if any, shank is built into the sole. If there is no mention of a shank, then there may not be one at all, meaning the boot will not be comfortable because it will not retain its shape once it conforms to the foot, nor provide support to the arch. Always look for a boot with a 3/4 or full shank.