The jury's still out on coffee in aggregate. Caffeine is a stimulant, and generally speaking, it has a host of positive effects on your processing speed, alertness, etc. Coffee may even have long-term positive effects there, though the evidence is inconclusive. Additionally, it might be neuroprotective.
There have been conflicting and sometimes contradictory reports on coffee's effects on cancer, cardiovascular disease, etc. Many studies suggest coffee has anticancer properties; other studies suggest it promotes certain types of cancer. Same thing with arteriosclerosis.
In terms of dependency, caffeine has been shown pretty conclusively to be habit-forming and dependence-forming. Almost anyone who's been a longtime coffee drinker and quits cold turkey will experience the side effects. But it's not clear whether coffee is doing you long-term harm, long-term good, or some combination of the two that nets out to being positive, negative, or neutral.
For my part, I've been drinking coffee every day since junior high. My stance is that it's been a net-positive in my life, regardless of what price I may pay later on. But that's one man's opinion. Not a scientific observation.
Also worth noting: coffee, marijuana, and alcoholic beverages are complex substances. There are active compounds in coffee other than caffeine. There are active compounds in alcoholic drinks other than ethanol. There are active compounds in weed other than THC. Studies that isolate the effects of any of these compounds aren't necessarily indicative of the effects of the substances themselves.