Well I have heard the comparisons between the two by many of my triathlon friends, running/swimming coaches, and several sports researchers. (Maryland the state I run in does not have many jav throwers so I'm running on assumptions on this one) Here is what I have come up with.
Most Likely to get hurt in: Run>>Jav>Swim
Most Intense Practices: Swim>>Run>>Jav
Ease as you get better: Jav (It's all technical)>>Swim (The better you get the higher % of recovery on turns you are able to have)>> Run (never gets easier)
Pain Levels during actual event: Run=Swim>>>>Jav
Most Likely to Die in: Swim>Run>Jav (someone may get in the way of the thrower)
Most "Fun": Jav>Run>Swim