This program by Pavel Tsatsouline might interest you:
According to the author, the 3RM progression is what you are looking for regarding weighted pull-ups.
On the interwebs there is a blogpost of someone who spaced the days out because it was too hard on the joints. As in 1 day on, 2 days off.
On that regard, Chad Waterbury offered this advice:
TL;DR Use rings if possible, and neutral grip as second best to spare the joints.
Personally I found that the lats are more involved in a pronated standard grip pull-up than in a neutral grip pull up where biceps take a more important role. So I prefer using a pronated grip if possible.
There is also the Easy Strength and Grease the Groove approach, promoted by Dan John and Pavel Tsatsouline.
Grease The Groove is performing the lift multiple times throughout the day, never even approaching fatigue, etc. More can be found online.
You most probably already know about all of the above, but I include it for completeness-sake for the lurkers that may stumble upon this post.
Hope that helps