There are various substances that you can place in bottles, however there are of course some that are more valuable then others. The trick is balancing the amount of hearts replenished; with staying alive to use what's in you're bottles. The following should always be kept in your bottles.
Medicine - there are a few different kinds of medicine that can be found throughout the game. Purple Medicine is by far the best because it replenishes all of your hearts, and will temporarily make Link stronger in a fight. Try and keep the Purple Medicine (or Great Fairies Tears) in most of your bottles.
Red Medicine is another great liquid that you can keep in your bottles, and will serve you a great purpose in the early game by replenishing 8 hearts. During the first three levels, and even on into the quest to find the fragmented Mirror of Twilight you should always try and keep your bottles stocked with Red Medicine. Another great thing about the Red Medicine is that it's free from killing Red Chu's and also if you dip it from the store near the lantern man (even though you're supposed to pay you can run away).
Blue Medicine will replenish most of you're hearts, but at a price. You can buy Blue Medicine for 100 rupees a bottle from the small Goron in Kakariko Village, but only at night. If you have the cash then I would defiantly opt to have Blue Medicine over the Red, but only in a form that you can buy it in. When you're out in the fields or in a dungeon don't drink the liquid that you can obtain from killing Blue Chu's in the wild. This liquid will appear to be like the kind that you buy from the Goron but in reality this Blue Chu Jelly will have the adverse side affect of taking life away from the use.
Milk is one other form of replenishing your life, but I would only recommend this if you're in the very early game. The nice thing about Milk is that it's cheap, and come in two servings, each replenishing three hearts. This is nice because it will save you time and money in the long run, but only until you get enough heart containers to make the Red Medicine effective. Milk will wear out its usefulness by about the third dungeon in the game (possibly before that) but is still nice to have on hand when first starting out.
Fairies - These small little creatures will be found all through the lands and dungeons of Hyrule. Make sure you take the opportunity when you see one to catch it in a bottle. These little winged creatures only heal Link by 8 hearts, but will revive him from being knocked out! This means that if an enemy has a really powerful attack you may not have been expecting and kills you before you have a chance to drink some Medicine, the little Fairy will come to you're aid! I would carry at least one or two in my bottles at all times, and they can be used at random as well (If you feel the need) just by using them like you would anything else you might keep in a bottle!
There are plenty more substance to keep in your bottles, but keeping them stocked with the above items is what I would suggest. In most cases I try and have two bottles of Purple Medicine and two Fairies, or three Purple Medicine and one Fairy. For more info on where to find the bottles hidden in Zelda Twilight Princess I have another guide written about their locations, so feel free to refer to that! Happy Hunting.
Published by Chris Tidwell
Student at a local college View profile
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