These are in no particular order, and some entries will show up in both categories for reasons which will be explained in due time.
The lack of weapon and armor restrictions -- this is by far my favorite innovation, since it allows Gandalf to have a sword. Of course encumbrance is more important now, but more on that later.
Specialists -- I'm a tremendous fan of Raggi's version of the Thief. I especially like that the Specialist is able to determine individual things it is good at, such as sneaking or finding food in the forest. It adds a certain amount of character customization without increasing the time spent making a character.
Common Activities -- These are dead simple and provide a framework for the Referee to use. This is true of most OSD&D systems, but Raggi has expressed it elegantly while still allowing every character to sneak and search and find traps (though they're not as good at it as Specialists who have focused in it are).
Weapons -- I love the Small/Medium/Large Weapon system. It reminds me of WFRP, and if D&D is my first love then Warhammer is the cheap floozy I'm cheating on her with. (2e if anyone cares, and I've always thought someone could make a really cool Lankhmar hack for it)
Encumbrance -- Some of you who read that Weapon/Armor restrictions are replaced by encumbrance probably winced due to the normally fiddly nature of Encumbrance rules. Raggi's are genius and dead simple, especially with his character sheet.
The Magic Book -- Some people may disagree with me, but I'm a huge fan of the way he has treated magic. Unlike Labyrinth Lord, it allows for experimentation at low levels and they're very easy to handle (at least from my read through). His spell descriptions also generally match up with the darker tone of Nightwick Abbey so I can use them almost whole sale.
Firing into melee -- it's mean and it should be.
Language Acquisition -- The rolling to see if you know a language thing appeals to me, even more so because I usually don't have all the languages set up in advance of a campaign, and can now add them on an ad hoc basis without the player's being handicapped by language choice at the beginning.
The good part is free -- Since I'm doing a dungeoneering based campaign, the Referee Book isn't terribly useful to me, and I'd just be using equivalent rules from other editions anyway. The part I'd use is free though, so if you were worried about price, remember you can still check it out.
Class Roles -- Each class has one thing it does really well, that the other class don't do at all or not as well. While the most famous example of this seems to be his interpretation of the Fighter, it's true of all the classes.
Edit: Ascending AC -- I know a lot of people don't like this, but I do. I hadn't included it initially because Swords & Wizardry also had it. If you don't like it, consider it a Con.
Demi-Humans -- The Demi-Human races are kinda sucky. This is most true of the Elf. I'm of two minds about this. One the one hand I don't really like people to play demi-humans but understand their inclusion in D&D. In this case Raggi's method is a stop-gap, but I completely understand someone who thinks that making them suck is not a good way to convince players to play humans. On the other hand, they suck. There is very little reason to play anything but a human, and they're basically an afterthought. Regular readers will know I've given some thought to the place of Demi-Humans in Nightwick, so this doesn't jive well.
Common Abilities -- I told you some would show up more than once. These are almost too good. I more or less let player's describe where they are looking and let that determine whether they find secret doors and such, either by modifying the d6 roll or just saying the players found the fucking thing. I know many Old Schoolers do the same, and it's one of the reasons I was attracted to OSD&D in the first place. Raggi's system is so good it almost becomes a unified mechanic. That makes it difficult to justify modifying it based on player input and their is another porblem...
The Specialist -- They can max out their skills, and pretty early if they do it right. They still have a chance of failing, but it essentially tells that character "you don't have to describe shit because you will find anything secret any time it comes up," which pisses me off.
The Price List -- I just don't like this. I know some people do, I don't. I don't mind a steep one, like AD&D's or Labyrinth Lord's, but this is too much.
The tech level -- This is easily remedied, especially if you're importing one another price list, but the assumed tech level of the setting is way to high for me. I prefer Antique to High Medieval technology in my D&D, not Early Modern. (Yes, I know the Empire in WFRP is early modern, that's why I specified D&D).
The flavor in general -- I know I can change this, but the feel of a game is very important to me. As mentioned above in the entry on magic, some of it really jives well with my setting; however, he's a bit too grim and dim even for me. I also find his write up of Fighters almost offensive, but I won't hold it against the man.
There is stuff I'm forgetting. I'm sure of it, but they'll probably come up in the comments.
Writing this has forced me to temper my position a bit. I'm thinking now that I'll try to figure out a way to integrate some of the aspects I like in S&W WB. I'm not entirely sure how successful this'll be but I'm willing to try.
For a while now I've been pondering doing a free downloadable supplement for the White Box that would be like Greyhawk or Blackmoor but for Nightwick. The largest problem I see with this is that I tend to steal from other Old School sources and forget where the hell I got it from in the fist place. I know I got it from somewhere but I don't really remember where. If I do create such a document it'll probably have some Raggi-isms in it, even if they are massively warped by my interpretation of them and the fact that they have to work with the white box.
(In case anyone is wondering, it'll be free because I don't have the money to commission any art, as well as a general principle that RPGs should be cheap if not totally free.)
Hope this is helpful.