Great question.
One thing to keep in mind is the range of the song. If it's a song where the lowest and highest notes are not that far apart (like O, Give Thanks [lowest note is the 7, highest the 6) then you can modulate frequently without pushing the range of your congregation or choir. However a song like Give Thanks w/a Grateful Heart spans a minor 10th (you do count both verse and chorus). There are only a few viable keys for a song with that kind of range.
Other than that - it's a matter of taste. Also, for small-ranged songs you can jump up a whole step or even a minor 3rd.