Sorry for rather newbie question. I am reading an Panel CookBook and how to create different layouts for homepage and other landpages. Apparently it is possible to achieve the same result with Panels models and template sub-theming and overriding. So my questions are: 1. When to use one of the above methods? 2. Performance issues Panels vs Theme overriding? Thanks.
I think the thing to keep in mind here is how the site is going to be used. If users are not going to log into it, it almost doesn't matter in terms of performance because you use Boost.
You can also use caching features in panels. I've never really noted a large hit for using panels on a website, as long as the layout is reasonable and the site does not have an excessive amount of modules on it. Panels exposes a lot of functionality, and you can pry it out of my cold dead hands.
If you've not used Boost before, do yourself a favor and commit to doing so!
NOTE: In your other question you referenced D7. Boost may not be ready for D7 just yet but you should keep it in mind.