First of all, its been proven via chromatographic analysis of smoke that there is no net decrease in tars by using a bong. The bong will filter out more active ingredients than tars. While there may be a functional advantage to a bong in cooling the smoke, humidifying it, or maybe just letting you take really huge hits, there is no medical advantage to a bong in terms of net loss of cancer-causing substances.
On what to fill your bong with, I think that's largely a matter of personal preference.
Hot steamy water is more humid, and I think that's probably the big reason why some people like it (less irritating). One possible disadvantage is that truly hot water might make certain bongs difficult to handle! Other people swear by ice water.
After having tried every possible variation over the years: quantity of water (a little vs a lot), room temp water, ice water, hot water, juice instead of water, just-ice-no-water, "air bong" (ie no water or ice; just bud) this is my take:
-My favorite way was probably a little bit of water and a lot of ice.
-More than an inch or so of water just makes the draw harder without any extra benefit of cooling/flavor.
-Juice and the like is a waste of time; stick to water.
-If the bong has a carb that lets you control air intake when drawing, then you can get pretty smooth hits with no water. Not much of an advantage to doing "air bong" otherwise.
Anyway, its so easy to try these things, I figure that anyone who actually owns a bong has already done so!