Well I tell you what I do, though I don't know that it's the best, but it is the best for me. I give x amount of hours per day to practice and then I divide that up amongst my pieces. Each morning I sit down and take two minutes to divide it out borrowing from some adding to others depending on what I feel needs to most work, what I have a lesson on, what I need to perform soon, ect. Another way of doing this would be to split them up into two groups and alternate so that you hit all your pieces every 2 days. I don't do this simply because I find myself thinking, "Tomorrow is the day to work on Brahms....sigh..I would rather work on it right now." I would rather hit everything all the time. Blame it on a short attention span if you will, but I'd rather spend 1/2 hr on each of two pieces than an hour on one, one day, and an hour on the other the next day. Here's sample (this is an extreme amount of practice, and I'm only doing this much because I'm a full time piano student who is cramming for an exam, just so you know).
Each day:
Bach Prelude 20 minutes (It's short and slow and I have a good handle on it, but I also plan to perform it next week so I don't want to give it only a few minutes).
Bach Fugue 40 minutes (This is also in good shape, but I wouldn't want to give it any less time because it is my most "worrisome" piece to perform and I want to make sure I really remember it, plus I need time to practice voices separately, and work on memory points throughout it, etc.).
1st mvmt of Schubert Sonata 7 minutes ish (pretty much done, just maintaining it until exam time and it's very short)
2nd mvmt of Schubert Sonata 25 minutes (I have to perform this next week, so even though it's only a few pages I want to really give it some extra time).
3rd mvmt. 1 hr, 20 min (This is my "beast")
6 Brahms' waltzes 45 minutes (that gives me less than 10 minutes a waltz, but they're not hard and I don't need to perform them for a bit yet).
Rach prelude 1 hr. 45 minutes (This is one of my furthest behind pieces and I aim to perform it next week - hence the ridiculous amount of practice time)
Bartok 8 min (also just maintaining until exam)
Chopin etude 1 hr (it's my least prepared piece)
I borrow and steal minutes where needed. After I perform the pieces set aside for next week, I'll steal considerably from them and add those minutes to the next pieces I plan on performing.
That's just to give you an idea what sort of factors influence what pieces get more or less time and how I divide it up. You can do this even if you just have an hour or two. Also, when I practice these pieces, since I have so much time, I do try to run through them once (I like to tape myself doing this and play it back to weed out the hesitations and blunders), but mainly I attack the "trouble spots" in them. For example, the first and last pages of my chopin are almost identical and I have a good handle on them so I would focus 90 % of my practice time just on the middle 2 pages. Sometimes I won't even play the first and last ones, and I rarely ever play the last one, cause why waste time on notes that were already covered in the first part. When I get closer to performing this I will run though the whole thing maybe once a day or once every other day, though. I also try to break up the pieces into sections. For example, in the 3rd mvmt of the sonata (alloted 1 hr. 20 minutes) I might spend 20 minutes on the exposition, 20 minutes on the development, and 20 minutes on the recap. The last 20 would go to whatever needs the most work.
Anyways, this is what works for me. I'm sure others would have suggestions as well.