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Apart from efficiency, it seems the two versions don't differ a lot in terms of features?
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There are many differences.
Links2 can hold around 5-6000 links (at the very most!)....Links SQL can cope with unlimited numbers of links, you are only limited by your hardware, but most dedicated servers should be able to work efficiently with a few hundred thousand links.
Links SQL also supports mod_perl which speeds up database queries due to persistant database connections and the Links SQL libraries being stored in memory rather than being loaded each request.
The email and newsletter options are also much more advanced as you can setup mailing lists.
The template editor is highly advanced and caches pre-parsed templates for faster loading and has the ability to restore original templates. You can also have unlimited numbers of template sets and load them dynamically using page.cgi?t=template_set
There is multi-language support via the use of language variables for each template set
It comes with mysqlman to allow you to manage your database quickly and efficiently should you need to.
One of the best features is the plugin system which can greatly extend and customize your copy of Links SQL and you can also share plugins with others and have them added to GT's download area (or sell them yourself).
There is an automated installer which lets you install Links SQL within minutes from your browser (or telnet) and even a windows app if you want to do the installation right from your desktop.
The build options are also more advanced allowing you to only "build changed" instead of building everything when you don't really need to.
There's a great category browser which allows you to easily manage categories and links...it's like an expandable and collapsible menu tree.
There is also static mode which turns your directory into html pages, dynamic mode which requires no building (page.cgi) and also the php frontend (page.php)
Shall I go on?