Jmeter is an awesome open source tool for performance testing websites and web applications. I like to use Jmeter for my performance tests.
I prefer to have an isolated phase for performance testing. I would never execute performance tests in development phase. The reason behind this being in the development phase there the project is not completely developed yet. You will have to develop stubs and drivers to replace the missing components to do a performance test on a module. Plus there are also bugs and issues in the functionality.
For an application or website to be ready for performance testing you first have to fix all the functional issues along with broken links and components. Performance tests make HTTP(s) requests to the servers and receive the response and during that they measure the duration, throughput, server health, etc. So for an HTTP(s) request and response to be successful you need to make sure that the functionality really works properly and there are not broken links and components. Hence, I prefer completing all my design and functional tests first and after that I move on to the Performance Testing phase.
If there is broken UI or functionality then all you will get in repose of a HTTP(s) request is a error messages and for broken links you will receive 404 errors. These are not really performance issues and hence you will not be able to analyse the performance for your application or website.
Happy Testing :)