It depends on what you are doing, to really answer this.
For example, if your cpu is busy on rendering an animated movie while use a javascript application you will see a slower performance.
If you have a very interactive site, that sends a lot of data back and forth, over a 300 baud modem, the application may seem slower.
The browser is important though, as IE8 for example appears to be slower than Chrome, based on these benchmarks:
http://www.lifehacker.com.au/2009/09/browser-speed-tests-chrome-40-and-opera-10-take-on-all-challengers/
Here is a dated article about javascript benchmark tests that explains each one well, and may help you understand javascript performance.
http://www.codinghorror.com/blog/archives/001023.html
If your application uses lots of pages and you d/l all the javascript, or the main ones, upfront, then yes, it will run faster after the first page, but that is dependent on how your application is designed. If you never reload a page, but do everything dynamically, then you won't get a benefit by having 20 script files loaded in the beginning.