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Akeeba Release System
Open source. Software is available at no cost; support and forum access to forum require a paid subscription. Joomla 2.5 native.

Attachments
Open source; available at no cost. Joomla 1.7 native; as of 1 April 2012 a version for 2.5 was in testing. Popular in Joomla Extensions Directory. Any author can attach one or more files to an article.

DOCman
Open source; $69. Joomla 2.5 native. Popular in Joomla Extensions Directory. Addons available. Full featured and complex, it is overkill for many needs but a favorite among power users.

jDownloads
Open source; available at no cost. Joomla 2.5 native. Popular in Joomla Extensions Directory. Addons available. Localized into multiple languages.

Phoca Download
Open source; available at no cost. Joomla 2.5 native. Popular in Joomla Extensions Directory. Addons available. Full featured; often compared favorably to DOCman.

Remository
Open source; available at no cost. Joomla 2.5 native. Popular in Joomla Extensions Directory. Addons available. Localized into multiple languages. One of my clients is a satisfied user.

REFERENCES
The Downloads category in the Joomla Extension Directory. There are so many that I narrowed my search to noncommercial extensions available for Joomla 2.5.