There are a good number of finishes available. They are listed below in approximate order of abrasion / corrosion resistance and price.
Conversion:
Bluing
Parkerizing
Coating:
Roguard
Black-T
Gunkote
Norrell moly resin / Armor-tuff
Plating
Nickel
NP3
Hard chrome
These are the most common aftermarket finishes. Which one to recommend really depends on your taste, budget, and the intended purpose of the pistol.
Personally I find bluing to be the most attractive on pistols, and it's also one of the least expensive finishes to apply and re-apply. Much the same can be said of Parkerizing.
Coatings work well if the gun will be exposed to the elements on a regular basis. They will show wear over time, however, and the coating must be blasted off and recoated to refinish.
Nickel and NP3 (a form of nickel) plating hold up better, but they will eventually show wear too. Hard chrome plating is about the ultimate finish for wear and corrosion resistance. It tends to be the most expensive as well, but it is nearly impervious to holster wear that will eventually mar all other finishes.
There are other finishes out there -- boron carbide, titanium nitride, etc. -- but they are not really widely available.
Regarding color: my personal thoughts are that the OD/black "CQB wannabe" color scheme is currently overdone. I am also not overly fond of two-tone guns, though I have seen some nicely done. A common thing to do on a fancier grade of gun is to blue the slide and chrome the frame. Ultimately the color choice is entirely up to you, since you are spending the money and you will have to live with it.