This is pretty lacking at the moment. I'll add to it as I run into things I feel are suitable.
Why are the nature/gender/shiny controls disabled?
The PID determines gender/shininess. It also controls nature for generation 4. If you specify a PID, one won't be generated, and therefore the controls are useless.
How many characters can my Pokemon nickname have?
The game limits it to 10, due to using a "hidden" character at the end to indicate the end of the name. You can use 11, but it may have weird effects in game.
Is PokeGen available for the Macintosh OS or Linux?
No. It never will be. You can use software like Wine to run it on these operating systems, however. Wine and similar software will not work for 4.0 and higher.
Can PokeGen be used on Windows 95, 98, ME, NT, or 2000?
No. Windows XP or newer is required.
My Pokemon won't work on WiFi battles. Why?
This is usually a Pokemon validity issue. (As in you did something wrong.) These problems aren't dealt with here.
Why won't Mystery Gift codes work on Black, White, Black 2, or White 2?
See the troubleshooting section below.
What are Wonder Card "used IDs"?
Every Wonder Card has a unique ID associated with it. When you receive a Wonder Card by normal means, the game flags your save file as having obtained the card and doesn't allow it to be obtained again if it's a one-time card.
Do I need to set the used IDs for cards I've obtained?
No. The game will function normally without them being set. Not having them set will make it possible to determine that your save file has been modified, however.
Why can't I export PGT files? (generation 4 so-called "gifts")
This format should never have existed, and therefore is only able to be opened, not saved, in PokeGen. (And only because the files already exist. I can't do anything about that.)
How does "To Tabs" in the Mystery Gift dialog work?
It's only available for full cards in generation 4 that have a Pokemon within them. It displays the raw data. There's no PID generation done. Some location data is shuffled around to display it more accurately, however.
You should not use this Pokemon data directly. They will not look like they came from the card.
I'm using a flash card (R4, Acekard, whatever) and my save file isn't able to be loaded, or has bad eggs in random places. What's going wrong?
Make sure the flash card is saving data in 4 megabit format. 2 megabits is wrong and will probably have mangled data.
How do I edit existing items?
Click to select the item, wait a very short time, then click it again and wait for the combobox to appear. This works identically to renaming a file. You can also use this same method to edit the item count.
Mystery Gift codes not working for Black, White, Black 2, or White 2
Note: These codes will not work for the non-Japanese versions of Black 2 or White 2 until PokeGen 4.0 is released.
Use the following checklist:
You only have one enabled Wonder Card code at a time.
The target game, that is, Options > Target game, is set to the correct game(s).
The code generator dialog has the correct game selected.
You're selecting the desired Wonder Card slot from the code generator dialog drop-down list.
You're attempting to activate the code after loading your save file in-game.
You're activating the code with the buttons you selected in the code generator dialog.
You're then opening the in-game menu, as in the menu where the save button is.
If you were already in a Pokemon center and the delivery NPC isn't there, you need to leave and re-enter.