Now when database is ready, it’s time for coding.
I will describe it basically, if you want any particular details - you can always ask me.
Site is written in PHP + MySQL, there are several PHP files: main file (index.php), configuration file, some helper classes and one file per module - I made it ‘think’ about each subdomain as module, e.g. for tag.myprogs.net it loads tag.php and so on. Kinda OOP 
All regular files (images, scripts, stylesheets) are loaded thru files.myprogs.net (configured in mod_rewrite).
Here is my .htaccess mod_rewrite configuration:
RewriteEngine on
Options +FollowSymlinks
RewriteBase /
RewriteCond %{HTTP_HOST} !^files.myprogs.net$ [NC]
RewriteRule ^[^.]+$ /index.php
Javascript is placed in both .js and .php files, all general scripts are in .js, and localization variables in .php
e.g. PHP code:
echo "var bad_program =\"{$Lang['program_bad']};\"";
And Javascript code in .js file:
if(bad) alert(bad_program);
Actually, you can check by yourself looking at files.myprogs.net/javascript/locale.php
I’m also using famous prototype library for easy scripting, for example I implemented suggest-like feature with it. When you add new program, it will suggest you already existed programs with similar name (LIKE query in MySQL is used here).