<p>I am working with a larger than average sqlite database (for use on both on windows and linux) and am looking to maximize the performance I get out of it. The database is to be installed on commodity hardware along with an sqlite gui. The users I am delivering this to are sql savvy but are unlikely to undertake their own optimizations (creation of indexes, setting of pragma etc.) so I am keen to get as much out of the box performance as possible (to ensure maximum usage of the data).</p>

<p>One issue Windows seems to throttle the execution of queries much more than Linux and another is that I am less familiar with sqlite's approach to indexing (compared to other databases such as postgres).</p>

Have you read the
SQLite Optimization FAQ
(a few years old, but still seems useful)?
I don't think 1gb is particularly large, even for SQLite.  It can certainly handle much larger databases stably.