Item description:

Be sure to always keep backups of your save files prior to editing. I'm not perfect, mistakes can exist in the program still.

This program can be used for Diamond, Pearl, Platinum, Heart Gold, Soul Silver, Black, White, Black 2, and White 2 for the following tasks:

Generating Action Replay codes to create Pokemon, modify the Pokedex, and add Mystery Gift data, including exporting to an XML file that can be dragged to the Action Replay code manager
Loading and saving of save files. Pokemon data and Pokedex data can be fully modified.
Loading and saving of party and PC .pkm files (136, 220, and 236 byte, encrypted and unencrypted)
Adding Wonder Cards to save files
Conversion of Action Replay codes into Pokemon information (This is limited.)
Finding a PID to match IVs, nature, gender, ability, shininess, and hidden power type/power - with variable IVs
Recalculating save file checksums
Editing items
Editing C-Gear background images

Most of what you need to know to use the program is self-explanatory. However, there are now tooltips explaining just about everything in it. There are some things that aren't quite covered though:

Windows XP or newer is required. (However, it does run without issues on "emulated" Windows programs for Mac OS and Linux.)
(This is only applicable to generation 4 games, and maybe not even HG/SS.) Using codes for party Pokemon can sometimes cause bad eggs upon activating the code. You can just activate it again and it should fix the problem. (You can check the summary after activating each time to see if it's fixed, or just close the party display and re-open it.) I don't think there's any way around this. As far as I know, this has no negative effect on the game when you save, as long as you don't save it with a bad egg. (I'm not even sure if saving with a bad egg would be harmful, but there's no reason to do so.)
Pokemon can be dragged around amongst party/box slots.
.pkm files can be dragged into and from party/box slots.
You can associate compatible files (save files, .pkm files, etc) with PokeGen to be able to easily load them from Explorer windows.
Holding alt and clicking a Pokemon icon will display that Pokemon's information instead of requiring you to right click and "View data".
Holding shift + alt and clicking a Pokemon icon will set the slot's data with the tab's data. Obviously this is equivalent to right clicking and selecting "Set".
If you don't want to receive updates to certain languages, delete the corresponding language file.

If you can't figure out how to do something, read the tooltips. For those that don't know, tooltips are an informative message that gets displayed when you stop your mouse pointer over a control (editbox, dropdown box, button, etc) for a short period of time.
There's also the questions and answers thread that's being updated occasionally.

Note the date on posts in this thread if you're reading through it. There were many changes to the program since its initial release, including a rename, removal of generation 3 support, and other major redesigns.
Also, this thread used to be the only way to post feedback/bugs for the program, prior to a forum section being made. That's why it has tons of posts when it's a locked thread.

--------------------------------

Future plans (These are things I'd LIKE to add, but may not get around to.)

Numerical mode for the species lists
An options dialog with more options to replace the expanding options menu list
A help file instead of tooltips
A format for storing multiple Pokemon in one file
Raw data viewing/editing