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I am using LinqConnect on Windows 8. Over time I get a large number of etilqs files in the folder where my database is. I know they are sqlite files, but what are they for, and will they just accumulate forever? I am concerned that my customers might get thousands of these files over time. Are they related to the settings on my data context?

These files are not related to LinqConnect or DataContext's configuration. This is the question of the SQLite connection parameters.

Please try changing the "journal_mode", "temp_store" and "temp_store_directory" parameters. They indicate the journal mode for databases associated with the current database connection and where temporary tables and indices are stored.

For example, you could try adding the following entry to your connection string - "Temp Store=Default".
Advanced connection properties are available via Database Explorer, right-click on Database Connection->Edit Connection Properties->Advanced.