Hibernate is a popular Object/Relational Mapper tool for Java, and implements the persistence API. Besides ORM functionality, it provides indexing and search, annotation-based constraints, OGM for NoSQL storage, various tools (mapping editor, console, wizards, database reverse engineering) and a few extensions (Hibernate Shards).
DocFetcher is an Open Source desktop search application: It allows you to search the contents of files on your computer. — You can think of it as Google for your local files. The application runs on Windows, Linux and Mac OS X, and is made available under the Eclipse Public License.
Yamado is a minimal note & journal system with extensions for functioning as a homepage & blog. Forget about databases, additional frameworks and the rest. Primarily intended to be installed on a server, requiring only standard utilities like bash, sed and awk. It uses the file system as a database. All articles are submitted as a file and stored as a file. The file format is YAML + Markdown.
Paperwork is a GUI to make papers easily searchable using OCR. The basic idea behind Paperwork is "scan & forget" : You should be able to just scan a new document and forget about it until the day you need it again.
FrostWire is a media manager and fast BitTorrent file sharing client. Its focus lies on searching files and a friendly user interface, automatically scans all Torrent indexers, prefetches torrent files and localizes contained meta data for better searching. It provides a built-in media library and audio/video player, allows to share contents per WiFi; and is also available as Android app.
LXR is a source code indexer and cross-referencer which generates HTML output linking to declarations and identifier uses within code. It's general-purpose and supports C, C++, Java, Python, Ruby, Perl, COBOL and other languages. It also works well with larger code bases, provides a search function, and understands versioned sources.