Lugia: Timid
Entei: Timid's fine
Suicune: Bold for a defensive moveset, Timid for offensive
Raikou: Timid, but you could probably make do with Naive if you don't mind a special defense drop
Latias: Timid
Ho-oh: Jolly's perfectly workable
Moltres: Modest's fine
Charizard: Modest can work with a Special set
Blaziken: Adamant or Jolly on a physical set, Mild or Rash on a mixed set. Never Modest
Empoleon: Modest would generally be the best pick
Typhlosion: Timid or maybe Modest
Feraligatr: Adamant
Giratina: Bold or maybe Impish, for Altered Forme at least
Sceptile: Timid, or Modest, or Hasty, depending on the set
Articuno: Timid or Modest on an offensive set, Calm on defensive
Zapdos: I would say Timid
Kyogre: Timid or Modest
Groudon: Adamant, preferably, but maybe Jolly
Mewtwo: Modest or Timid.
For the movesets and stuff, so you can make the decisions more easily and such, go here. That's what I generally do.