I know SQLite's SQL query engine is implemented as a VM. Are there ways of optimizing repeated queries, similar to compiling a query to avoid the VM churn? Perhaps more importantly, have you ever been disappointed by the query engine's performance?
You can prepare a query to use multiple times (if you are using the C interface, at least; as far as I know the command-line interface does not support this), as another comment mentions. You can also prefix a SQL statement by EXPLAIN to view the VDBE codes. But, I see that sometimes the VDBE code is not as good as it should be.
You can put each query and the result of preparing that query into an LRU cache (or even just a static pointer in C if your application only ever deals with a single connection). Then you can reuse these without preparing them over and over.