There is two most difference between use a bong and a joint, the first one is the filtration, the second is the amount of steam you can inhale all once,  

when  you doing it with a bong, it is  allows more smoke to buildup and be inhaled at once.

many things are happening when using a bong,  with cooling, each inhalation, the water (or other liquid) inside the bong filters out the ash that would otherwise end up in your mouth, such as when smoking a joint or pipe. There’s also a certain amount of tar that is filtered out of each hit as well, which is why bong water eventually turns a sickly brown after numerous uses.

research conducted in California have shown that bongs filter more water-soluble psychotropic phytocannabinoids than tar and polucarbons, which means the user has to smoke more marijuana to get an effective high, because the tar:phytocannabinoid ratio is now more skewed towards tar. The amount of research on the effectiveness of bongs and bubblers is very low, and as such, an air of speculation and debate surrounds the effectiveness of these tools.

the Pro and cons when you use rolling paper,

Pros: low cost, and very easy to do, Just tear a small piece of rolling paper and make it. Smoke up slowly as you enjoy every inhale whenever, wherever. No hassle in carrying it to places.

Cons: When you smoke a joint your are inhaling byproducts from the paper also. Less Tetrahydrocannabinol out of the stuff

Bongs:

Pros:You only inhale the material you are smoking. most the time the perculation filter built in the bong are filter out the tars, ash, you will get less residues and more steams,  than smoking the same amount through joints.

Cons: a glass water pipe may costly, from honorand to thousands, they are not easy to carry and very fragile , make alot hassles when you want to use it outdoor, 

they both are the most popular common folks use in the present days, choose what to use, it really just depend on your situation and your pockets.