It's been awhile since I finished it (over ten years, I'd guess), but I recall Star Ocean 2's system being pretty fun.
That's all that comes to mind. I don't craft at all in Kingdoms of Amalur Reckoning, it overpowers your character to the point of godhood.
Edit: Just remembered Shining Soul 2 on GBA, a nice little mix of Diablo and the Shining Force series. Yoou can loot rare gems and ores of differing quality and craft weapons and gear (with random stats), as well as loot other even rarer items to create even rarer gear.
Definately the Atelier series, especially the new ones. It looks pretty normal: find recipe, find materials or ingredients, synthesis/craft, bingo. However, the details of crafting itself is awesome. It has quality that determines the nature of the items, traits that you can insert, attributes, etc. How awesome is it that with some efforts you can make an item that can heal HP, heal MP, revive, buff ATK/DEF/SPD, cure status abnormalties, auto-activated when HP reaches certain HP point at once? Or weapons that can deal all elemental damage, status debuffs, buffs, increase special skills damage, etc at once. Well, the game is about crafting so that's to be expected.
3 things I dislike before a game release: The wait, the haters and the trolls
I'll tell you what crafting system I DON'T like, and that's the one in Cross Edge. Absolutely ridiculous system, they designed it to be as tedious, time consuming, and annoying as they POSSIBLY could.
I'm kind of partial to the way FFXII did it actually. Go out and gather materials, and then trade them to a crafter, and you get the item. No muss, no fuss, really simple to use.
The Atelier system is kind of fun too, but I REALLY hate that most of the "Endgame" items are so limited. Like, in Atelier Iris, a lot of the ingredients to make some of the later items are extremely limited in quantity. Like you only get 3 Golden Cogs or some such, and you can never get anymore. I really dislike that.
I sometimes feel as though life is a curse that has been placed on the living. I envy the unborn at times.