<p>Which search engine would you recommend for a Commerce website?</p>

<p>We have millions of products in a catalog and we want it to be as quick as possible.</p>

<p>We would also want to make sure that the marketing driven through the search engine will be fast and effective.</p>

<p>What are your opinions?</p>

This is only half the answer to your question. I've used it with Java and not .NET. Fast is said to be the better search engine. I don't know. However for Commerce Endeca is considered to be the best. I've used it with a catalog of 5Mil. products and queries are very very fast.
If you use .NET or Java does not matter in the end solution the Search Engine stays the same. 
And what search engine to be used is not answered easily. it all depends on what you want/can spend. My experiences with Endeca are very positive.