[Shirt] For the most part, you can be pretty safe picking up a plain white buttondown from a department store for this costume. If you aren't concerned with how accurate the shirt is underneath the sweater, you just need to get a collar in the right shape... some button downs have buttons on the tips of the collar, and you want to avoid this. You also want to avoid collars that are too skinny. The other thing to look for, is probably a shirt of poplin or cotton. You need to be sure it's not shiny or an optic white.
But, if you want a shirt that's accurate all over, here's my observations on the shirt. The best place to observe the shirt itself, watch the scene in Prisoner of Azkaban during Hagrid's first class. Though it might seem like you can just pick up any old shirt from the store, there are subtle differences in shape, and if you keep an eye out for the details, you should be able to find one in the store that comes close, or, make your own. The first thing to note is that girl's shirts are not fitted. They are the same shirts the guys are wearing, and even have the buttons on the right like guys shirts. I've learned from looking that it's nearly impossible to find shirts with these specs in the women's section, so it would probably be best for girls to look in the boy's and men's department for the shirt. The bottom dips down in the back (I don't know the technical terms for shirts like this, if anyone knows, I'd be appreciative to know!) The front can't just have buttons, it must have a button placket, topstitched. There is a pocket on the left front of the chest. I've noticed (please check my reference image) that a few people have pockets with flat bottoms, and some have pockets with slightly pointed bottoms, so either are acceptable, just not too pointy. Pay close attention to the collar shape, you may want to print off the reference picture to take with you to compare. The collar is topstitched, and if the one you buy isn't, it's an easy fix. For the sleeves, there are two small pleats in the sleeve at the cuff (standard width cuff it looks, 2 inches most like) but be sure that it isn't a full sleeve, these look to be pretty straight. There is also a topstitched placket here, and is also topstitching around the armhole. The back of the shirt has a yoke, and I note most people have a box pleat in the center, but on Ron and Dean, there are two smaller tucks on the outer side of the yoke.
[My Shirt-making notes] I am making my own shirt because the men's shirts were way too big and I couldn't find any in the boys departments. For this I am using McCall pattern 2447, view C. This pattern is for a men's button-down shirt. I think it will work, I am using the small/youth size. My chest measurement is 32" and the one for this size is 34", so it should be about the right amount of looseness, and if it's too much I won't have to take in much. The pattern goes up to a XXX-Large, 56" chest, so this pattern should work for everybody. I think just the collar shape has to be adjusted a bit, otherwise, their flat sketch looks a lot like mine (SEE COMPARISON). The pocket needs to have a slightly pointed bottom (though square will do, if you look at the ref pic, one kid has a square pocket) but that's easy also. Right now I am in the process of starting the shirts, I'll document my alterations.
[09/13/07] Done with the shirt! I will be bringing a tutorial for shirt alterations for this particular patterns. Taller/bigger girls can probably get away with the man's shirt mostly as is with slight sleeve and collar alterations, but smaller/petite girls like me will need to heavily modify the shirt to make it the correct size. I definetly advise making a muslin of the shirt to see how the fit compares with the movie. Here's my completed shirt with my Ravenclaw Tie:
[Tie] Ties for PoA on are in the darker school colors, with two thick bars next to each other and one skinny one. WizardTies.com has movie-accurate fabric for the ties, but I found their ties to be a little clown-like big. Be aware of the official WB release ties, they are actually incorrect. I know the hue of the Gryffindor tie is a purpley hue that isn't correct, and they print the house crest on each tie, which is also incorrect. The tie is made of silk.

There are several places easy to find via google to buy the incorrect "official" silk tie, but for those looking for a more accurate, but polyester tie can find them through Ebay Seller Accent1222. Unfortunatly there is no "buy now" option, but it looks like there are regular auctions for ties set up so chances are good you can lay your hands on one for a pretty good price. I found this tie, though the fabric had thicker ridges and was over-all thicker than silk would be, had the correct shape.

[THE SKIRT] The skirt is actually very easy, it was just very hard to find a clear shot of it to figure out what is going on! The skirt is a basic A-shaped skirt. It's a wrap-around, and has the illusion of having two large inverted box-pleats in the front, with one of them being the opening. If you look at my sketch, you'll see that the back is just a basic A-shaped skirt, some flare but not too much, just enough to move in. I haven't seen many back-shots of the skirt, but I don't think there is a back seam, or darts. However, everyone's body shape is different, so you may need to have a back seam, or better yet, two small darts in the back. The front will be in two pieces, with the right side overlapping the left. Your box pleats will start a little farther out from the Princess Seam. Each side will be the same size when pleated, but the left side will only have one pleat and the right will have 2, forming an inverted box pleat. I have found that a 2 1/4 inch deep pleat seems to look about the same as the movie skirt (meaning there is 4.5 inches to the whole pleat, since it is folded in half, and 9 inches total for the box pleat). There are two pleats that meet each other, meaning an inverted box pleat. You will want to iron and pin in your pleats before you can shape the waist. In [THIS PICTURE OF HERMIONE] you can see a gold button above the pleat and I assume there's one on the other side for symmetry, since the opening is technically disguised in the pleats. My sketch above is the correct shape of the pattern, except I drew the skirt almost split into thirds with the pleats but the front panel is actually a bit bigger. For size reference... my skirt is 26.5 inches at the waistband (sits about 2" below the natural waist), and the front of the skirt measures 15.25. The panel in the front is 9 inches across... so the center panel will take up 2/3 of the front.
The fabric I ordered from [FASHION FABRICS CLUB]. I can't direct link what I ordered since they don't carry regular stock, they get things in lots. They had a lot of different shades of grays, so it's good to browse, and compare it to pictures of the sweaters on WizardKnits.com to try and match the color. Remember, colors on a monitor can be different than actual fabric. Also, if you order from Fashion Fabrics Club, be aware that they don't have shipping options and they send it by the slowest, cheapest option possible. Their customer service isn't great either, but they have good prices. The fabric I ordered was 60" wide, and I needed 1.5 yards of it. Charcoal is usually the color to look for for the skirt.
The pictures below show how the skirt opens, they're lightened so you can see the detail. Also, my pictures of my finished skirt. The first one of me shows it compared to Hermione's skirt.
Here are my pictures of the skirt for reference. The ones I captured will be marked, there are others I got from The-Leaky-Cauldron.org, which is a GREAT site for research.