A: Sources for covering knees:
1. Pri Megadim, Orach Chaim 75; Mishbetzot Zahav, letter 1, and Mishnah Berurah, letter 2: The shok extends from the knee upward, hence below the knee poses no problem wherever women customarily leave it exposed. (quoted in Women and the Mtzvot, volume 2 by Rabbi Getsel Ellinson, P. 187-188)
2. Hazon Ish, Orah Hayyim 15, letter 8: ….Hence the shok of Berakhot 24a must connote the thigh. The Talmud would then not be dealing with below the knee, and its laws would hinge upon custom, as P’ri Megacim wrote. It is difficult to rule conclusively. (ibid).
We see from the above that from the knee upwards is assur regardless of minhag hamakom. According to the Mishna Berurah, below the knee depends on the minhag hamakom. The Chazon Ish is unsure if below the knee depends on minhag hamakom or if it’s always assur.
B: short skirt with stockings:
Responsa Yabia Omer, Vol. VI. Yoreh Deah 14, letter 1: Nylon stockings do not constitute coverage because they are transparent and the skin is visible through the fabric. (R’ Ellinson, p. 190)
C: short skirt with socks/tights that cover the knee:
1. R’ Shlomo Zalman Auerbach and Rav Elyashiv: “to cover the knee whether standing or sitting and not to rely on the fact that the socks are covering” (Mesila, 5730, p. 97 quoted in Halichos Bas Yisrael, chapter 4, footnote 24) (note: It uses the word “garbayim” which I am assuming means socks or tights and not sheer stockings but I may be wrong about that.)
2. I believe that Rav Moshe Feinstein has a teshuva on this as well. I don’t have an Igros Moshe, but if the place where I will be for Shabbos has one, I will bli neder try to look it up.
D: Wearing Pants (without a skirt):
1) Responsa Avnei Tzedek, Yoreh Deah 72: “…1)There is no intention to resemble men, and 2) they are different from a man’s. Both here and in Poland, even pious,modest women have long practiced this, without a complaint being heard.” (R’Ellinson, page 261-262)
In footnote 126, R’ Ellinson, writes: “Clearly, Avnei Tzedek is not dealing with the kind of trousers worn by women in our day, but with special loose-fitting work trousers, devoid of any fashion significance”
2) Rav Eliyahu Henkin also poskened that it is muttar for women to wear loose pants.
3) Responsa Yaskil Avdi, Vol V, Yoreh Deah 20: “…For a different reason, however, they should be forbidden to women. Trousers are a wild, promiscuous and immodest garment for women, since the legs are separated from each other…: (R’Ellinson, p. 263)
4.”In any event, we may distinguish between tight and loose fitting trousers. Avnei Tzedek saw nothing immodest about the latter, and Yabia Omer makes such a distinction as well. Another factor that must be taken into account, however, is the existence of a community of modest Jewish girls with their own standard. The fact that they are careful to wear only skirts, affords significant weight to this stricture. By wearing a skirt, a Jewish girl identifies with this group and separates herself from other more permissive circles.
To a certain extent, in the last few decades the skirt has become a sort of “yarmulka” for the scrupulously observant girl who strives to follow our sages’ ethical guidelines, as refelected in their halakhic rulings. By her refusal to wear trousers, she demonstrably declares that she is unwilling to resign herself to the dictates of modern style, and that she takes exception to the immorality so rampant these days in society at large.” (R’ Ellinson’s footnote 129 on p. 263. Please note that R’ Ellinson is not a Poseik and I don’t know how accepted his seifer is although it does have a haskama from Rav Ovadiah, zatsal, so his take on things does not necessarily constitute daas Torah – this footnote is his own opinion.)
E: Skirt above knees but knees covered by pants:
I don’t know since I never saw any sources on it (it’s a pretty new issue, I think) and I never asked. My svaras that on the one hand, one should not walk around with pants with a knee-length skirt over it, but on the other hand, it is okay to wear a long skirt with pants under it if her knees might show while bike riding, etc. were based on logical conclusions from the above sources on the issue of wearing pants in the first place.
However, they were only my own svaras, and I do not know what the poskim say and no one should rely on them for a psak halacha, and I might be wrong. (but I brought these sources because I wanted to show where I was coming from).
edited