Trying to sort through the various TV Specials and OVA's for Pocket Monsters can be quite a difficult task.  TV-Tokyo often advertises the airing of Pocket Monsters movies and Mini-Movies as specials, making many people think that "Oh, Special #5 is the third movie."  Here's what I understand the various specials to be, and hopefully I can clear up some confusion:

1998/1999/2000/2001

Japanese Title:  Boku-tachi Pichuu BURAZAAZU" (We Pichu Brothers) & Nyaasu no Heya" (Nyasu's Room)
Air Date:  July 12th, 2001

Again, I really don't know anything about these titles.  If you have any info, please e-mail me.

Japanese Title:  "Pikachuu ga Ippai!" (Full of Pikachu!)
Air Date:  August 12th, 2001

I know absolutely nothing about this special.  If you have any information, please e-mail me.

Japanese Title:  "Pikachuu no Fuyuyasumi KOREKUSHON" 

(Pikachu's Winter Vacation Collection)

VHS/DVD:  December 19th, 2001

This DVD collects the first three "Fuyuyasumi" videos all in one set ("Pikachuu no Fuyuyasumi Yori," "Pikachuu no Fuyuyasumi 2000," and "Pikachuu no Fuyuyasumi 2001"). 

Japanese Title:  "POKETTO MONSUTAA KURISUTARU:  Raikou Kaminari no Densetsu" 

(Pocket Monster Crystal:  Lightning Raikou's Legend)

Air Date:  December 30th, 2001 (Japan) It's the long-awaited Pokemon Crystal special!  The special takes place outside of the regular story following Satoshi and focuses on Kenta, a Bakufuun trainer from Wakaba Town.  Kenta was given a Hinoarashi by Utsugi-Hakase, and his pokemon is at a very high level with almost invincible attacks!  Marina, who aspires to be an "Idol Trainer," has a Mumaa, an unusual Ghost-Type pokemon with a cute face.  Fans will notice that Kenta looks just like the protagonist in Pokemon Gold/Silver while Marina looks just like the female protagonist in Pokemon Crystal.  The special also has Jun'ichi, a boy who has a crush on Marina. And you know with new heroes, you also have new villains!  Adding to the roster of Rocket-Dan members are Bashou and Buson (both named after famous haiku poets), two members who are at an elite level way beyond Muashi and Kojirou.  Bashou, the blue-headed one, has a cool criminal mind and is the "Rocket-Dan's Number One Handsome Guy," while Buson, the blonde,  is incredibly strong and intelligent.  The two perform a special "Rocket-Dan Tag Battle," which I can only assume to be a regular tag-team battle.  The third guy in the picture is Shiranui-Hakase, the most powerful Rocket-Dan scientist in history!  He uses the "Crystal System" to attract electric pokemon, particularly Raikou.

The basic plot is that Kenta and Marina, two trainers who are good friends, reunite at a Pokemon Center to see how much their skills have grown since they last parted ways.  Suddenly, a huge thunderstorm appears, and Rocket-Dan members Bashou and Buson emerge from their underground hideout near the Pokemon Center.  Using Shiranui-Hakase's "Crystal System," a device that lures electric-type pokemon by emitting huge currents of electricity, the duo plans to lure all sorts of electrical pokemon to them.  Then, using their "Chicken Walker" mecha, they'll snatch the weakened pokemon up and deliver them to Sakaki!  Kenta and Marina discover their plan and Kenta jumps up to stop the mecha when a bolt of lightning knocks him back!  A loud rumbling is heard, and Bashou announces that the Rocket-Dan's plan has succeeded--they've lured the legendary pokemon Raikou into their clutches!