I do not have favorites, but have used these ...

Novello orchestral reduction
http://www.amazon.com/Messiah-George-Frideric-Handel/dp/0853602115

Dover organ continuo
http://store.doverpublications.com/0486260674.html

A hardback copy of the Novello edition (or the Schirmer, according to taste) is particularly useful. (Not a rebound version of the paperback edition.)

I turned said pages for literally dozens of performances by various semi-competent choirs accompanied on organ by my first main high school organ teacher, who paid for his family's Christmas and their summer vacation each year by hiring himself out for Messiah gigs on a strictly cash-and-carry basis around Christmas and Easter. I'll probably have those pages, especially the tricky turns and cuts, imbedded in my brain unto my earthly end. And what caterwauling accompanied the meticulous organ-playing! Egads!

Believe it or not, Lorenz has an edition whose pages correspond to the Schirmer Edtion, and is quite a bit cheaper. I prefer using the Watkins -Shaw for solos
but most church choirs are already familiar with Schirmer for choruses. I have a friend who is an editor, composer for Lorenz so got a bunch of cheap copies a few years ago. Can't remember the editor-well-qualified guy who just recently died. My mind is going- two glasses of Prosecco before dinner will do it every time.

For whatever it may be worth, I just use the piano reduction and "arrange" as I go along. I've found that if I don't like the layout, voicing, etc, of an organ edition it becomes more distracting than it's worth.