Parasite Eve Secrets
Here is a bunch of secrets from Parasite Eve.  I have tested or done all of these so if done correctly, they should work.
Junk Weapon:

Out of the few secrets in this game, this is the biggest.  You may have noticed that many enemies drop pieces of junk when you beat them.  It may seem to be useless, but there is really a great use for them.  If you go to Wayne, he will offer to take your junk if you have any.  So when you do get some junk, go to Wayne and pick "Discard Junk" from the dialogue options that come up.  DON'T discard it like you would other items for they would just go to waste.  Keep collecting junk until you get to 300 pieces (I know it takes a really long time).  To help you collect junk, you can go to the park and fight those birds for one, or you can fight the birds at the bottom floors of the Chrysler Building too (it is a bit faster, but you have to be in the EX game to get there.)  Put many of your bonus points into your inventory so you can hold more junk without having to go back to Wayne so often.

Now, when you do get your 300 pieces of junk, Wayne will exclaim something realted to the amount of junk you have given him.  Then he will offer to make you a gun.  You can either choose it yourself, or you can let Wayne choose it.  Unless you've saved immediately before, I would suggest letting your own fingers do the picking since Wayne has a chance of turning your huge junk collection into one big piece of "Super Junk" (useless)!

When you get to choose, you will get to choose from the following:

Handgun
Shotgun
Machinegun
Rifle
Grenade Launcher
Rocket Launcher
Leave it to Wayne

And here is what you will get depending on what you choose:
Choice:

Handgun
Shotgun
Machinegun
Rifle
Grenade Launcher
Rocket Launcher
Leave it to Wayne
Leave it to Wayne
Leave it to Wayne
Leave it to Wayne

Leave it to Wayne
Leave it to Wayne
Weapon:

DE50AE7
M10B
P90
MAG
HK40
LAW80
PPSh41
SP1C
USP-TU
AK-47
Attack:

125
121
122
152
116
220
80
120
116
155
Range:

56
70
53
185
70
210
76
69
88
154
Bullets:

17
7
200
21
9
1
71
20
31
24
Rate of Fire:

x2
x3
x10
x2
x1
x1
x10
x2
x5
x5
Slots:

8/9
4/7
5/7
4/7
6/6
0/0
2/6
2/6
3/9
6/8
Attributes:

none
Burst
Random Shot
Critical Bonus
none
none
none
none
Counter
Counter + Critical Bonus
Super Junk (Useless)
Duper Junk(Also Useless)
I would suggest that you pick the rifle.  Read on to find out why.

Ultimate Weapon:

After you have collected 300 pieces of junk, go to Wayne and he will make a weapon for you.  Pick the rifle and you will get a MAG.  Now, use trading cards and Mod Permits to get more slots on it.  Then you should find and add the following abilities to the MAG:

Command x2 (Upgrade to x3 later)
Critical Attack Bonus(It should already be on the weapon)
Burst
Quickdraw
Tranquilizer
Acid
Cyanide

Be sure to use a super tool to take the 2x rate of fire ability off of the weapon.  It only makes it do less damage.  Pump all of your bonus points and weapon bonuses into your new weapon.

Don't put any affects such as Freeze or Fire rounds because it may heal some enemies.  The affects that I have listed above will only hurt enemies that are weak against that attribute.  They will not heal any enemies.  Also, don't put any multiple shot abilities such as x2, x5, x10 ect... because the damage done is divided between the bullets.  You should now have an ultimate weapon that can kill just about anything.  And if you put enough bonus points into it, you can breeze through the game with ease.  My weapon has 751 Attack, 444 Range, and holds 262 Bullets.

EX Mode:

All you have to do is beat the game, then save your game when it prompts you to after all of the credits.  Then, when you return to the main menu, a new option will appear called "EX Mode".  Select that and load your saved data.  EX Mode is slightly harder than the regular mode except you gain access to the Chrysler building.

Chocobo Banner:

Square has secretly 'snuck' the famous chocobos from the Final Fantast series into Parasite Eve.  On the New York Map, select the Museum.  Select it only once, then wait until the camera zooms in on the front of the building.  If you look at the blue banner on the Museum, you can see the outline of a chocobo on it.

Infinite Ammo and Medicine:

On about day 2 or 3, you can go down to where Wayne is in the NYPD #17th District and there will be some treasure chest.  One small one on the counter with ammo in it, and another on the floor with medicine in it.  They refill every time you leave the NYPD.  So if you just keep leaving and coming back, you can get infinite ammo and medicine!  As you progress through the game, the items you get are upgraded.  Early in the game, you will get Ammo+6 and Medicines.  Later you will get Ammo+30 and Medicine 3s.

Early Ammo:

Near the beginning of the game, right after you beat Eve for the first time, go up to the hole and Aya will make a decision over wheather or not to jump down the hole.  Pick "Forget it" and go outside to where you first started.  Talk to the officer out there and he will give you Ammo+15.  Keep repeatedly talking to him and he will give you up to 60 ammo.

Infinite Trading Cards:

When you're at the Hospital in the room where you save the nurse at, at the very top side of the room there is a cabinet that is turned on its side.  Look behind it and you will find a Trading Card.  Look behind it again for another, and another, and another...  You can fill your inventory with them, but if you try to leave and come back for more, they will be gone and you won't be able to get any more of them.

Earning Bonus Points:

You can earn more bonus points if you fight a bunch between level-ups.  The goal is to dodge the enemies' attacks.  The ideal place to fight is the Chrysler Building where the enemies give pity experience.  The other way is to keep beating the game in EX Mode.  You get BP each day and also when you beat the game.

Super Armor:

When you're in EX Mode, go to the Chrysler Building and when you get to floors 61-70, you can find the Cr-Armor 2.  It is the best armor in the game.  Now that you have it, free all of the slots (should be 10) and put the following attributes on it:
Max-HP Up
Attack Up
Auto Medicine
Auto Cure
PE Light
Resist Confusion
Resist Stiffness
Resist Poison
Resist Darkness
Item Capacity +4

That's it.  Just put all the bonus points that you don't put on your weapon on this and you should be nearly invincible in no time!  My armor is up to 400 Defense, 222 PE Energy, and 191 Critical.  One thing to note, after I got done creating my "Super Armor", Wayne offered to engrave it for me!  And no, I wasn't talking to Wayne on the Crusier, I was at the NYPD.  Strange...

PE Jumpstart:

If you use your PE Energy a lot in a battle, it will eventually start to recharge slower.  When it does start to slow down, change your armor and it will be like new.  Also, it will recharge normally if you die and get revived by one of your "Revives".

Rare Trading Cards:

In the Chrysler Building, you will find some 'Special' trading cards.  If you take them to Wayne, he will allow you 2 upgrades for the price of one card.  When you find and give about 12 to Wayne, he will give you a 'Tool Box' which is like an unlimited supply of Tools.  If you find and give all 14 to Wayne, he will give you a 'Super Tool Box' which is interestingly enough an unlimited supply of Super Tools.  If you find all 14 cards and you beat the game and start it over in EX Mode again, Wayne will still have the cards and when you talk to him after he talks to you about his card collection, he will give you another 'Super Tool Box'.  The cards you should find are as follows:
  P38 Trading card
  B-Hawk Trading card
  Kasul Trading Card
  PPKS Trading card
  M1 Trading card
  MK5 Trading card
  MP44 Trading card
  BAR Trading Card
  MG42 Trading card
  M29 Trading card
  M73 Trading card
  Type 38 Trading card
  Type 3 Trading card
  Eagle Trading card

Helicopter Cam:

To get a close up view of New York, press "Select" at the New York map to get a view from the helicopter that flies around.

Energy Shot:

If you're at a really high level (39+) Energy Shot actually does more damage than Liberate.  Trust me, it takes a
really long time to get to that level.

Chrysler Building Tips:

Everyone who plays Parasite Eve knows, or should know know about the Chrysler Building.  If you don't, it is the one place that is unlocked when you replay the game in EX Mode.  It is a long tedious maze of hallways and more hallways.  Here are some tips and info that should help you with your quest through it:

- The Chrysler Building's floors are completely random.  Therefore, I cannot give you a walkthrough for it.  So when navigating it, try these strategys:
     1.  First look for the 'Item Room' on each floor.  If you find the stairs before the Item Room, go back and find it.  Don't count on remembering which levels you missed because there are far too many to remember.  To help find the Item Room, try going east or west over north or south when you have a choice.  This will also find the elevator.
     2.  After you find the Item Room, go look for the stairs to the next level.  It may help to go north whenever you have a choice too.
     3.  Develop a really good short-term memory.  If you don't already have one, this could be tough.
     4.  Patience Grasshopper...
- There is a boss every ten levels.  They are as follows:
     Level 10 - Arachnid
     Level 20 - Alligators
     Level 30 - Centipede
     Level 40 - Triceratops
     Level 50 - Cockroach
     Level 60 - Crab
     Level 70 - Queen Bee/Workers
     Level 77 -  Maya (The Original Eve)
- After you beat a boss, use the key that you get to go back down via the elevator.  Go to Wayne and drop off your stash for safekeeping, and save your game.  Then return (using the elevator) and continue.
- Every 10 levels, the music changes. (Not necessary to know)
- There are no save phones in the Chrysler Building.
- The later bosses (Level 50 up) tend to get really hard.  Be sure to prepare yourself before battle.
- If you manage to get to floor 77, you will fight The Original Eve.  This is one boss that dosen't mess around.  One tip though--Try not to attack Eve while her 'Little Helper' (Maya?) is in the screen.  If you do, she will put some kind of ailment on you and heal Eve (Not good).  When or if you do beat her, you will be rewarded with the second ending to the game! (Yeay! Whoops...spoiler)
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