All you need to do is cement the window and go over with a fine hair (natural bristle) brush.
The more you buff it the darker it gets.
Here's a video I made of a finished window...
Avoid using too much whiting that tends to strip the patina, Instead let the window set over night then buff to a dark glossy lead finish.
<a href="http://www.youtube.com/watch?v=fmH3K43ujmc" target="_blank">http://www.youtube.com/watch?v=fmH3K43ujmc</a>

What are you talking about? you always agree with me. You just like to find the smallest loopholes in my posts to tear me a new one 

Now that's scary!

Here's your chance to be at your best... I also find how fluxing the window can result in a blotchy appearance.
I use a 3" cheap paint brush, the kind with a wooden handle you find for $2 at Loews or Home Depot. I then intentionally cut the bristles to half their original length. This is now my flux applicator/lead cleaner. I don't just apply flux at the joints but rather vigorously go over the entire panel scrubbing the lead as I go. I only do an area I can solder in less than 15 minutes or so. Leaving (hydrochloric) flux on too long somehow makes soldering tougher and you need to reapply it.
Once soldering is complete I then use an old cloth rag and thoroughly wipe excess flux off the window while all along distributing flux residue throughout the whole panel. I believe this etching process of the whole window may be the reason for the incredibly uniform finish I get.
In contrast... i have witnessed students using those cheesy little flux brushes applying flux only to the joints quite sparingly. The end results (lead finish) is very blotchy. This is even more evident when using a zinc border. Be sure to flux the entire length of zinc not just where you plan to solder. Not a heavy amount of flux but more like a fine film of it. You will be amazed how uniform acid patinas take to this as well. To insure a even better finish, go over the whole zinc with a green scrubby pad with the flux still on it.
Basically... Blotchy looking finishes are caused by the inconsistent application of acids and or oxidation prior to cementing.
I'm sure there are other factors but these are the 2 most common.
To correct a blotchy window you could try cleaning it with a scrubby pad or actually go over it (vigorous but slow scrub) with a hydrochloric based liquid flux using the brush mentioned earlier. Let it sit for an hour or so then wipe down and cement again. The cement will act as a neutralizer so don't worry about the acid from the flux. When cementing... resist using too much whiting to clean/dry the window right away. Use sparingly and let the panel dry at least 6 hrs before you buff it. When finished, allow to thoroughly dry/set overnight before you do the other side.

Ok, I need some instruction.  I do almost all my work in foil, and I brush the flux liberally over the piece.  I don't intentionally get flux on all the glass, but I don't try to stay off the glass either.  After I do both sides, I wash it in hot water in the bathtub with dishwashing soap, and scrub it clean with a stiff bristle brush.  That's it.  I let it dry, wipe the spots off with a cloth, and hang it up.  Sometimes I use black patina juice applied with a scrap of t-shirt after it has dried from the first washing. 
So tell, obi-wan, do i need to use whiting?  Or linseed oil? 

Again, Gary and I agree. The original post was about lead.
Foil's a whole nuther ball game.
Solder over foil needs good cleaning and neutralizing + wax and elbow grease.

Try to use 50/50 solder on leaded panels. You will notice it blends better than 60/40. My joints are exactly the same color as the lead when done using no patina at all except the cementing and buffing process. Patina as well (acid) will deteriorate the cement too...

Again talking about foil work ... sorry about the hijack ... what do you use for cleaning, neutralizing, and wax?  Johnsons Paste Wax?

Cleaning and neutralizing - CJ's Flux Remover, Neutra 5000, or Kwik-Clean.  Waxing - Clarity Stained Glass finishing Compound.

What I like about 50/50 solder on lead is...

1. It doesn't drip down under the leaves as much as 60/40 (minimizes breakage).
2. You can heat up the lead more to get a very uniform and smooth joint with 50/50.
3. The minimal shine to it than 60/40 (blends with lead)
4. The cost. And finally...
5. Discrediting all of the "pros" who claim 60/40 is for lead work. (I never understood that one) These same folks insist that glass needs to be grind for foil to stick and a bunch of other silly theories. The simple reason using 50/50 to avoid breaking glass by far a good enough reason to use it alone.

60/40 has a more fluid consistancy and will pass by the top leaves quicker than 50/50. If you have a "T" joint there is a greater chance of solder dripping around into the core channel of the lead and creating a button like pressure spot on the glass. This results in a greater chance for breaking glass moving the stained glass window (flipping etc.). Using 50/50 you can heat the lead came more so and get a more biting joint. I hope that was a good way to explain it. All along minimizing dripping of the solder.
The only option may be for flat lead where you may not want to heat the lead up so much so 60/40 may be a personal option here.
As for foil work I totally agree 60/40 is by far the better chioce for both it's higher strength and delicate flowability.