Well, I've not played Extra or Tsukihime, so I can't comment on those, but my answer for Fate/Stay Night is obviously HF True.
Simply put, aside from the fact that I much prefer Sakura x Shirou to the other two pairings, HF True is also the only ending in which Sakura is certain to have the chance to live a normal and happy life. Whilst I would like to think that Rin and Shirou would find a way to save her in the other two routes, until that is confirmed I am not overly fond of them. Further, HF True is IMO the happiest ending overall, since it is basically UBW Good but with Sakura saved, Ilya getting a less horrible death (and some happiness prior to that) and Rider swapped for Saber (which IMO is a good swap, although I doubt you would agree...).