Though there are hundreds to collect, Atelier Iris mostly avoids the collect-a-thon, pack rat mentality; each item has some use or can be synthesized with anoter to create something new. There are a few perfunctory shops that serve only as a place to buy and sell, but for the most part, shops also have that synthesize option, where your shop keep buddy can take items and forge equipment and healing items. Each one tells you what unique items she can make and what ingredients are necessary, also a cheeky way for the game to tease you with all the fancy trinkets that are still beyond reach, or taunt you with the fact that this is stuff you should've found by now.
Once you've synthesized an item, you can add it to the store's shelves for purchase and then try synthesizing again with different items from to make it stronger or create something totally unforeseen, though within a limit. For example, an item may require "powder" for synthesis, but a listed substitute can be "red powder" or "green powder" and anything that can't go with it isn't listed. Though forcing what can and cannot be mixed may be limiting, it's definitely needed. Have you seen the open-ended mixing system in something like Thousand Year Door or a Star Ocean? Freedom is nice, but restriction is vital to not overwhelm, and then repel, the player.
Secrets of Mana
Atelier Iris is a slice of fried gold for a side quest nut like myself, a majority of them deriving from the synthesis system. Every time you're in the shop and something new is available for synthesis, charming little conversations between the shop keep and party members occur. And the first time the item is synthesized, there's a wrap-up conversation, an excellent way to introduce and expand side characters even if they have no bearing on the main plot itself (I've still no idea what prompts a new item to be added to the synthesis list, though this does makes the game feel natural and spontaneous). You're practically never informed where to find these items necessary for synthesis, and this DIY-whenever attitude allows the game to float along leisurely. Even the plot is in no hurry: the first half is about a green alchemist named Klein Kielsing trying to find Avenberry, a legendary haven for alchemists back when there was plenty of mana to go around.
Warriors join, misadventures ensue, and as the party approaches Avenberry, you realize that nothing epic has really happened - just your party exploring every horizon, run-ins with the army and rebels, finding and creating items, forging relationships with shop keeps, stumbling into optional odd jobs - and you should also realize that this game shouldn't be any other way. I almost dreaded going into Avenberry because (and I bet this is the kind of dread every designer hopes for!) because it felt like the game was going to end. An overall conflict does begin to present itself after Avenberry, which becomes extra disappointing when it turns out it's a textbook case and a total yawn (rebel alchemist...thinks he can control all of the mana...world domination, and so on).