I have retired from MMD and uninstalled the program.

My advice to anyone reading this is: DO NOT USE MMD!
The user base is obsessed with ROOLZ and DRAMA, and most model and accessory
file downloads are now encumbered with password games and ridiculous rules of use.

However, if you wish to use the program, here are a few links to get you started.

You can download the MMD program from the Vocaloid Promotion Video Project site.
Scroll down to the "MikuMikuDance (DirectX9 Ver.)" link and download that ZIP file.
(A 64-bit version is available, but I have experience with only the 32-bit version.)
Extract that ZIP file to C:\Program files\, a folder on your desktop, or anywhere you like.

"MikuMikuEffect" is a separate download. The latest version is available from this VPVP page.
Scroll down to the "MikuMikuEffect Ver number (date)" link and follow it to the download link.
Extract the DLL files from that ZIP file to the same folder that contains MikuMikuDance.exe.

To use models (PMD and PMX files) and accessories (X files), drag-and-drop them over the program.
Just play with some different models for awhile, and you'll soon learn how to position and pose them.

The MMD program can create pictures by itself. From the menu, choose File > Render to picture file
The picture should be saved as a Windows BMP file that can be edited in programs such as Paint.NET.

I installed x264vfw to render videos to 1280x720 H.264/MPEG-4 files.
I used both VirtualDub and Avidemux to edit and splice video files.

For further help, see Learn MMD, or just "Google It You Moron"...

DOWNLOAD MODELS AND ACCESSORIES AT YOUR OWN RISK!

bowlroll.net/up/

citrusmoothie.tumblr.com

deviantart.com/?q=MMD+download

3DCGモデル&MikuMikuDanceフリー素材集

mikumikudance.wikia.com/wiki/Category:MMD_Models

nicovideo.jp searches, most recent first:
MMDモデル配布あり (models)
MMDアクセサリ配布あり (accessories)
MMDステージ配布あり (stages)
MMEデータ配布あり (MikuMikuEffects)
MMDモーション配布あり (motion)

seiga.nicovideo.jp searches, most recent first:
MMDモデル配布あり (models)
MMDアクセサリ配布あり (accessories)
MMDステージ配布あり (stages)

Some of the dic.nicovideo.jp lists:
MMDユーザーモデル (MMD user models top page)
MMDユーザーモデル(初音ミク関連) (Miku Hatsune models)
MMDユーザーモデル(meiko関連) (Meiko models)
MMDユーザーモデル(kaito関連) (Kaito models)
MMDユーザーモデル(巡音ルカ関連) (Luka Megurine models)
MMDユーザーモデル(鏡音リン・レン関連) (Len & Rin Kagamine models)
MMDユーザーモデル(GUMI関連) (Gumi models)
MMDユーザーモデル(亞北ネル関連) (Neru Akita models)
MMDユーザーモデル(弱音ハク関連) (Haku Yowane models)
MMDユーザーモデル(vocaloid関連) (other Vocaloid models)
MMDUTAUモデル(重音テト関連) (Teto Kasane models)
MMDUTAUモデル(デフォ子関連) (Defoko models)
MMDUTAUモデル(桃音モモ関連) (Momo Momone models)
MMDUTAUモデル ("A,I,U,E,O" UTAU models)
MMDUTAUモデル(か行) ("K" UTAU models)
MMDUTAUモデル(さ行) ("S" UTAU models)
MMDUTAUモデル(た行) ("T" UTAU models)
MMDUTAUモデル(な行) ("N" UTAU models)
MMDUTAUモデル(は行) ("H" UTAU models)
MMDUTAUモデル(ま行) ("M" UTAU models)
MMDUTAUモデル(やらわん行) ("Y,R,W,N" UTAU models)
ACMMD (Armored Core MMD)
進撃のMMD (Attack On Titan MMD)
ダンガンロンパMMD (Dangan Ronpa MMD)
MMD C CLUB (Dream Club MMD)
fate/mmd (Fate/stay night and related)
MMD銀魂 (Gintama MMD)
APヘタリアMMD (Hetalia Axis Powers MMD)
MMDiM@Sモデル (Idolmaster MMD)
ジョジョの奇妙なMMD (JoJo's Bizarre Adventure MMD)
MMD艦これ (Kantai Collection MMD)
MMDらき☆すたモデル (Lucky Star MMD)
MMDまどか☆マギカ (Madoka Magica MMD)
MMDワンピ (One Piece MMD)
MMD薔薇乙女 (Rozen Maiden MMD)
MMD戦国BASARA (Sengoku Basara MMD)
MMDタイバニ (Tiger & Bunny MMD)
MMD東方モデル (Touhou Project MMD)
MMDゼルダ (Zelda MMD)
MMDユーザーモデル(漫画、アニメ関連) (manga/anime models)
MMDユーザーモデル(ゲーム関連) (game models)
MMDユーザーモデル(その他ジャンル:人型) (other human models)
MMDユーザーモデル(その他ジャンル:非人型) (other non-human models)

And if you really want them, the Internet Archive has copies of the old mikudance.info listings.
Please do not reprint the old listings elsewhere. They are incomplete and full of dead links.

Good luck.