I've been getting a lot of questions on how to progress on the tricky parts of Phoenotopia, so to alleviate my inbox, I'll start listing them here. Refer to this if you're really stuck! (If you have a guide you'd like me to link here, PM me)

============ Other Awesome Guides ============

A more comprehensive guide by nggroundsplayer347
http://www.scribd.com/doc/237933823/Phoenotopia-Guide

============ CHAPTER 0 : Miscellaneous ============

Q: Are there missables in this game?
In Zelda fashion, no. If you think you've found a missable item, PM me.

Q: My green bracelet is gone!?
The green bracelet disappears because I didn't have a slot for some key quest items. So the green bracelet will temporarily leave your inventory when you're carrying the bandit or the golem head. But don't worry! Just by continuing your journey, the green bracelet will return! As for why I chose to the slot of the green bracelet, it's because the gift that Aella gives you can't be taken advantage of until later (by which point you should have the green bracelet back).

Q: I'm using a 360 controller and the up/down is inverted?
I am aware of such an issue, and Tom Fulp was actually the first to tell me about it. The conclusion we reached is that the error lies in the flash version of your browser. In Tom's case, the up and down were inverted on Chrome but worked fine in IE. The up and down works correctly for me.

So this one is a hard one to tackle - there hasn't been too much noise about this issue, so I'm inclined to think the current Up/Down on the analog is the correct configuration for most people. I recommend trying it with a different browser to see if you have different results. If there is enough noise about this, I will put this higher on my priority queue, but for now saving problems are.
 

============ CHAPTER 1 : Panselo & Duri Forest ============

Q: Why is the slingshot so weak?
It's more of a stunning tool. That bat should be your bread and butter.

Q: How do I defeat frogs?
Frogs hop at the same rate, height, and distance every time, so it's possible to know where they'll land. Stand at a spot you know they'll appear before and charge up your weapon to defeat them in one hit! Later when you get the slingshot you can also stun them.

Q: How do I cross the gap in the temple ruins?
First shoot the switch to extend the bridge to your side. Once you cross the bridge, hit the switch again to extend the bridge to the other side. Then stand on the edge of that newly moved bridge, and shoot the switch on the next platform to bring it over to you. Basically hit the switches twice!

Q: How do I defeat the Armored Toad Boss?
Shoot the Duri Fruit patch above him or bouce a sling rock off the wall behind him to hit his back. Doing so will get him to turn around revealing his weak back side.

Q: How do I cross Atai Bridge or crawl through small spaces?
You need to buy a "Scroll of Rolling" back at the Panselo Dojo. This will allow you to roll through the small spaces.

============ CHAPTER 2 : Atai and the Bandits Lair ============

Q: How do I get the bandit in Atai's jail to reveal the Bandits' Lair?
Buy a Talkinator potion from the potions witch and give it to him.

Q: How do I get bombs?
Talk to Lisa and ask her about "interesting places to visit?". She'll reveal to you Adar's house where you can then find bombs.

Q: How can I make some money?
A woman in Atai's market place will buy Duri fruit from you. Also the man at Honey Bee Labs will buy Honey Combs from you.

Q: How can I get more health items?
If you're strapped for cash, there's a spot in Duri forest that has 3 healing fruits you can collect. The fruits will respawn if you leave the area to the world map, so it's possible to get a lot.

Q: How do I defeat the Sand Dragon?
Youtube Video
To dodge him effectively you can clear out his lava pools with bombs. You can also whack his spitfire in the air to cancel it out (but that's a risky maneuver). To dodge his roll attack, try to roll under it as it's coming. Also helps if you have the hammer, since you'll do a lot more damage. Feed him a bomb when he's burrowing underground and snapping at you to stun him and make him vulnerable to your attacks.

============ CHAPTER 3 : Thomas's Lab, Daea, Dungeons, and the Prince Tower ============

Q: How do I enter Thomas's Lab?
The first room of his house has a switch hidden beneath a box on the left wall. Shoot the box to reveal the switch. Then shoot the switch. Click here for a picture.

Q: How do I defeat the robot in Thomas's Lab?
Video Here
He has only a few different patterns of laser attacks. Once you learn to dodge them, it's simply a matter of pushing him over the chasm and flipping the switch.

Q: How do I access the sewers?
After Thomas has been kidnapped, to access the sewers, you need to talk to a sequence of NPCs in this order:
1. First is the maid in the upper right most room of the inn. She says she saw Thomas get dragged away.
2. Then the guard in jail (lower left most area in Daea). He tells you to talk to the king.
3. Then the orange haired little girl outside the castle gates. She says that a person named "Ruby" could get you into the sewers. Her apartment is the middle residential area.
4. At Ruby's apartment, is a man who tells you Ruby went to buy lunch.
5. The store keeper at the food shop tells you Ruby just left for the sewer.
The sewers will now be opened.

Q: How do I access blocks A, B, and E of the dungeons?
There's a prisoner you can rescue in Block D. He tells you of a weak floor in Block C. Use a bomb where he tells you and you can get into Block E, which contains keys to reach the other blocks.

Q: How do I navigate the ladder obstacle course in the tower?
Watch this video 

Q: How do I defeat the Kobold boss?
Youtube Video
Generally stay on the opposite corner of where he is so that you can respond quickly to his change of direction. Place a spear on the wall ahead of time so that you can quickly move up or down. When he charges his blue ball of death attack throw a spear into the opening of his shield. If he's hanging upside while charging, you need to hop to throw the spear in. Finally, make use of charge attacks - they do double damage and can hit up to 3 times in a row if you're spamming the attack button hard enough.

============ CHAPTER 4 : Beyond the Wall ============

Q: How do I defeat the Big Eyed Boss?
Link to video
Big Eye follows a set pattern of 5 phases. Learning how to handle and dodge the attacks of each phase and you will survive.

To do damage effectively however, you want to wait until the right phase. When you close the 4 smaller eyes he'll open his big eye but only for a set amount time. So if you open his big eye at a bad time and there are a lot of distractions on the field, you will have squandered your chance to damage him.

The best phase to do damage is the 5th phase when he's shooting 2 giant laser beams since there are no distractions on the field if you're standing in front of him. So it's best to close 3 of his smaller eyes, and then wait for his 5th phase, before you close his 4th small eye.

Q: How do I outrun 66?
As you are running away from him there are switches you can hit to close the doors. Every door you close on 66 delays him and buys you more time. If you hit a switch to open a door, there is usually a switch to close that same door. If you open it, don't leave it open!

Finally hit the switches using your jump attack, since that is a lot faster than your sling shot. You should only use the slingshot to activate a switch once during this whole chase sequence.

Here's a video

============ For Completionists ============

Q: How do I access Forgotten Forest?
Collect 30 moon stones and the teleporter in Fran's lab will be activated.

Q: What is the scope of the Heart Ruby and Moon Stone tracker in the world map selection screen?
It extends to all obtainable collectables if you were to enter from that map location. There are two problematic areas where the scope is really broad because they have secret paths connecting many areas. The first big area is Atai and the Bandits' lair which are connected by the well passage. The second is Daea and the Prince Tower connected by the Dungeons.

Q: What are the non-quests (ie the dead ends)?
- There is no quest behind feeding the Perro bird in Daea
- No quest behind the fake love letters in Daea
- There's no quest to get a Sand Dragon egg (there were plans, but they did not pan out)
- There's no quest behind the abducted Harpy. That's for the sequel.
- The door you see when running from 66 can not be accessed.
(Will add more non-quests as they come to my attention)

Q: How often does Chocolate Protein Shake work? How many Heart Rubies are there?
Five times. To get 99 HP you need to find all 23 heart rubies. That gets you to 89 HP. From there five protein shakes will get you the rest of the way to 99 HP.

Q: Tips for getting the speed run medal?
- The only heart rubies you should get are the ones that bosses drop. Any other one is too big a detour.
- Plan a smart route for which money chests to grab. You only want to get just enough for the key quest items (lamp, float donut, & roll scroll). For example, in Duri forest it's better to grab the money chest going back from the first boss when there are no enemies, then before.
- The only non-key item I bought was the hammer. 
- Sweet stamina boosting items like honey make a big difference in areas like Misty Gorge, where fast recharging stamina allows you nearly limitless jumps in water.
- If you die, refresh the browser to prevent the game from overwriting your save time or number of deaths.
- Expect it to be hard.

Speed Run Ch 1

Speed Run Ch 2

Speed Run Ch 3

Speed Run Ch 4

(I will update this news post as I get more questions.)