Windows:

Pros:

• 對ASP.NET、MS-SQL、Access支援度較高
• 能執行幾乎所有Linux能執行的軟體

Cons:

• 較易受到病毒及駭客攻擊
• 價格較貴
• 比較容易crash
• 較耗效能

Apps that run better on Windows:

Umbraco website building software

nopCommerce shopping cart

BlogEngine net blogging system

Linux:

Pros:

• 較穩定
• 較便宜(OS免費)
• 安全性較高
• 較不耗效能

Cons:

• 對ASP支援度較低，不穩定

Apps that run better on Linux:

WordPress blogging system

Magento shopping cart

Joomla website building software

參考資料：

1. https://www.quora.com/What-is-the-most-common-operating-system-of-web-servers-today
2. https://www.quora.com/What-OS-will-you-choose-for-Your-Web-Server-Windows-or-UNIX