Wanderer's Friend has some good crafting, and is probably the most complete crafting mod available. I do use a watered-down version of it that doesn't affect creature/material definitions (which the mod does) that will work easily with other mods, in case you already have a bunch of other mods installed and are too lazy, like me, to go and fiddle with all those creature/material/tissue files and whatnot in order to make the mods play nice. If you don't already have a total conversion mod or something of the like, then you probably have no reason not to use the full version of Wanderer's Friend.
For magic, I have one uploaded myself that currently doesn't have many conflicts, as long as you don't have a mod that changes creature_standard.txt. Or if you already do, then you can cut creature_standard.txt out of my mod before extracting it, and it won't override that other mod's changes. You can find it
here. Go nuts, but I warn you; take elemental mages and shamans/witchdoctors as a serious threat, because they are!
There are a bunch of other magic mods on the DFFD, and some more listed on the forums.
I had another one in mind, but you'll have to wait a moment while I try to find the damn thing again.For making the other races use towns, you can simply edit the files yourself. It's really quite quick and easy, and I can show you how to do it. Keep in mind that in the next update, Toady will be re-adding all the other sites, making these modifications obsolete.
If you want some new races to play with, check out the
Vilous mod by Darklord92; he's done a really good job, and they're fairly fun to play with.
You can't currently add more skills, and there's not really a whole lot you can do with them currently mod-wise, other than make more weapons utilizing the skills and giving creatures and playable races natural starting skills/varying skill learning/rust rates. I have no idea whether affecting relationships is currently possible without straight-up hacking the game with DFhack.
[Edit]
Found that other magic/secrets/werewolves n'shit mod again; it's
Fear the Night!