This list likely isn't complete.  But I thought it might help as a general starting point.  I'll also try and revisit this again at some point.

Online

Dream Baseball (ドリームベースボール)

Perfect 9 (パーフェクトナイン)

Pro Yakyu Legend Nine (プロ野球列伝『レジェンドナイン』)

Pro Yakyu Team Tsukuro Online 2 (プロ野球チームをつくろう！ONLINE 2)

Consoles (Sorted from newest to oldest)

Pro Yakyu Spirits 2010 (プロ野球スピリッツ)

Release: 4/1/2010
Developer: Konami
Platform: PS3, PS2, and PSP
Official site
Amazon JP PS3, PS2, PSP

Kodawari Simulation Pro Yakyu DS 2010 (こだわり采配シミュレーション お茶の間プロ野球DS 2010年度版)

Release: 4/1/2010
Developer: Now Productions
Platform: Nintendo DS
Official site
Amazon JP

Netto Powerful Koshien (熱闘パワフル甲子園)

Release: 3/18/2010
Developer: Konami
Platform: Nintendo DS
Official site
Amazon JP

Power Pro Success Legends (パワプロサクセス・レジェンズ)

Release: 2/25/2010
Developer: Konami
Platform: PSP
Official site
Amazon JP

Pro Yakyu Famista DS 2010 (プロ野球 ファミスタDS2010)

Release: 3/25/2010
Developer: Bandai Namco
Platform: Nintendo DS
Official site
Amazon JP

Power Pro Pocket 12 (パワプロクンポケット12)

Release: 12/3/2009
Developer: Konami
Platform: Nintendo DS
Official site
Amazon JP

Power Pro Yakyu Portable 4 (実況パワフルプロ野球ポータブル4)

Release: 9/17/2009
Developer: Konami
Platform: PSP
Official site
Amazon JP

High School Baseball DS (高校野球道DS)

Release: 7/23/2009
Developer: Spike / NIHON CREATE
Platform: Nintendo DS
Official site
Amazon JP

Power Pro Yakyu Touch (パワフルプロ野球 Touch)

Release: 7/21/2009
Developer: Konami
Platform: iPhone, iPod touch
Official site

Batting Revolution (バッティングレボリューション)

Release: 7/16/2009
Developer: Alpha unit
Platform: Wii
Official site
Amazon JP

Pro Yakyu Team Tsukuro! 2 (プロ野球チームをつくろう! 2)

Release: 5/21/2009
Developer: Sega
Platform: Nintendo DS
Official site
Amazon

Power Pro MLB 2009 (実況パワフルメジャーリーグ2009)

Release: 4/29/2009
Developer: Konami
Platform: Wii, PS2
Official site
Amazon JP Wii, PS2

Power Pro Yakyu 2009 (実況パワフルプロ野球2009)

Release: 3/19/2009
Developer: Konami
Platform: PS2
Official site
Amazon JP

Power Pro Yakyu NEXT (実況パワフルプロ野球NEXT)

Release: 3/19/2009
Developer: Konami
Platform: Wii
Official site
Amazon JP

Sunday x Magazine Netto! Dream Nine (サンデー×マガジン 熱闘! ドリームナイン)

Release: 2/26/2009
Developer: Konami
Platform: Nintendo DS
Official site
Amazon JP

PC / Windows

High School Baseball Simulator 3 (高校野球シミュレーション3)

Developer: CapyWorld
Windows 98/2000/XP
Site

High School Baseball 2 EX (高校野球道２EX)

Developer: NIHON CREATE.
Windows 98/Me/2000/XP
Official site

High School Baseball Girl's (高校野球道Girl's)

Developer: NIHON CREATE.
Windows 98/Me/2000/XP
Official site

Apache Baseball (アパッチ野球道)

Developer: NIHON CREATE.
Windows 98/Me/2000/XP
Official site