Depends on exactly what kind of boat you're building. I've used old fashioned, two part resorcinol glue, epoxy, Titebond, and even PL 500. A lot of guys are using 3M 5200 with a lot of success.
The resorcinol is a two part, dry catalyst/liquid resin, quick drying, waterproof, hard setting, and pretty much bullet proof glue. I'm not sure it's even available anymore though, or where to even find it. It a little difficult to work with. You have to mix as you go, the leftovers harden in about ten minutes, the joints have to be tight, and it is pricey. Probably some of the best you can by however.
Epoxy is pretty good. It is probably the most commonly used of all the adhesives, and it has to be mixed just like the resorcinol glue. It too is a hard setting glue, which means it dries hard and solid. It will gap somewhat, meaning the joints don't have to be totally tight. There are many variations and even some additives that can be used with it to increase it's versatility. With the correct prep, epoxy will even stick to just about anything.
Although I haven't used it in boat building, Titebond is awfully popular for all kinds of woodworking. I use it all of the time, just never used it in boatbuilding. The joints have to be tight, takes about twenty four hours to harden, is advertised as water resistant, and can be cleaned with water. (before it sets-up).
Even though not really recommended for this purpose, I built a layout boat using mostly PL 500 and am very pleased with the results. I haven't seen any PL 500 lately though. It may have also gone the way of the dinosaur. PL 500 was rated for outdoor use. It was nice to work with. Very economical, it came in both the 10 oz., as well as the quart sized caulking gun tubes. It is strong, will gap, is not a real hard setting type of adhesive, and had fairly long working time. A drawback however, was the setting time. I wouldn't trust it until it set for a couple days at least. It probably doesn't reach full strength though until about a week.
Probably one of the newest glues to reach the market is 3M's 5200. It's made specifically for Marine work. It too comes in 10 oz. gun tubes. It is a soft setting glue, will gap a little, but takes a while to set up, and is kinda pricey. I bought some for my latest project. I think I paid about $12.00 a tube. So far, I've used four tubes.
I'm sure some of the actual smart guys on here will chime in with their thoughts to help confuse you even more than I did, but I tried.
Good luck!
Jon