I'll edit this to add as many other pertinent issues as I can, although I wish the OP would address my comment above. I speak from several years as a professional online game developer and many more years as a hobbyist online game developer, for what it's worth.
Online games imply some sort of persistence, which means that you have broadly two types of data - one is designed by you, the other is created by the players in the course of play. Most likely you are going to store both in your database. Make sure you have different tables for these and cross-reference them properly via the usual database normalisation rules. (eg. If your player crafts a broadsword, you don't create an entire new row with all the properties of a sword. You create a new row in the player_items table with the per-instance properties, and refer to the broadsword row in the item_types table which holds the per-itemtype properties.) If you find a row of data is holding some things that you designed and some things that the player is changing during play, you need to normalise it out into two tables.
This is really the typical class/instance separation issue, and applies to many things in such games: a goblin instance doesn't need to store all the details of what it means to be a goblin (eg. green skin), only things pertinent to that instance (eg. location, current health). Some times there is a subtlety to the act of construction, in that instance data needs to be created based on class data. (Eg. setting a goblin instance's starting health based upon a goblin type's max health.) My advice is to hard-code these into your code that creates the instances and inserts the row for it. This information only changes rarely since there are few such values in practice. (Initial scores of depletable resources like health, stamina, mana... that's about it.)
Try and find a consistent terminology to separate instance data from type data - this will make life easier later when you're patching a live game and trying not to trash the hard work of your players by editing the wrong tables. This also makes caching a lot easier - you can typically cache your class/type data with impunity because it only ever changes when you, the designer, pushes new data up there. You can run it through memcached, or consider loading it all at start up time if your game has a continuous process (ie. is not PHP/ASP/CGI/etc), etc.
Remember that deleting anything from your design-side data is risky once you go live, since player-generated data may refer back to it. Test everything thoroughly locally before deploying to the live server because once it's up there, it's hard to take it down. Consider ways to be able to mark rows of such data as removed in a safe fashion - maybe a boolean 'live' column which, if set to false, means it just won't show up in the typical query. Think about the impact on players if you disable items they earned (and doubly if these are items they paid for).
The actual crafting side can't really be answered without knowing how you want to design your game. The database design must follow the game design. But I'll run through a trivial idea. Maybe you will want to be able to create a basic object and then augment it with runes or crystals or whatever. For that, you just need a one-to-many relationship between item instance and augmentation instance. (Remember, you might have item type and augmentation type tables too.) Each augmentation can specify a property of an item (eg. durability, max damage done in combat, weight) and a modifier (typically as a multiplier, eg. 1.1 to add a 10% bonus). You can see my explanation for how to implement these modifying effects here and here - the same principles apply for temporary skill and spell effects as apply for permanent item modification.
For character stats in a database driven game, I would generally advise to stick with the naïve approach of one column (integer or float) per statistic. Adding columns later is not a difficult operation and since you're going to be reading these values a lot, you might not want to be performing joins on them all the time. However, if you really do need the flexibility, then your method is fine. This strongly resembles the skill level table I suggest below: lots of game data can be modelled in this way - map a class or instance of one thing to a class or instance of other things, often with some additional data to describe the mapping (in this case, the value of the statistic).
Once you have these basic joins set up - and indeed any other complex queries that result from the separation of class/instance data in a way that may not be convenient for your code - consider creating a view or a stored procedure to perform them behind the scenes so that your application code doesn't have to worry about it any more.
Other good database practices apply, of course - use transactions when you need to ensure multiple actions happen atomically (eg. trading), put indices on the fields you search most often, use VACUUM/OPTIMIZE TABLE/whatever during quiet periods to keep performance up, etc.
(Original answer below this point.)
To be honest I wouldn't store the quest requirement information in the relational database, but in some sort of script. Ultimately your idea of a 'requirement' takes on several varying forms which could draw on different sorts of data (eg. level, class, prior quests completed, item possession) and operators (a level might be a minimum or a maximum, some quests may require an item whereas others may require its absence, etc) not to mention a combination of conjunctions and disjunctions (some quests require all requirements to be met, whereas others may only require 1 of several to be met). This sort of thing is much more easily specified in an imperative language. That's not to say you don't have a quest table in the DB, just that you don't try and encode the sometimes arbitrary requirements into the schema. I'd have a requirement_script_id column to reference an external script. I suppose you could put the actual script into the DB as a text field if it suits, too.
Skill requirements are suited to the DB though, and quite trivial given the typical game system of learning skills as you progress through levels in a certain class:
table skill_levels
{
int skill_id FOREIGN KEY;
int class_id FOREIGN KEY;
int min_level;
}
myPotentialSkillList = SELECT * FROM skill_levels INNER JOIN
skill ON skill_levels.skill_id = skill.id
WHERE class_id = my_skill
ORDER BY skill_levels.min_level ASC;
Need a skill tree? Add a column *prerequisite_skill_id*. And so on.