I use a lot of JQuery and normal javascript on my sites. Mainly I use validate, auto form fills, sliders, lightbox, loading php files in elements etc.
I have searched the web but cannot get my head around this. Will I be affected by the new chrome policy about NPAPI and Java?
http://blog.chromium.org/2014/11/the-final-countdown-for-npapi.html
Despite the name, JavaScript is not related to Java at all. JavaScript got its name because its first versions were due to be released at around the same time as Java's, and the marketing team at Netscape (the company where JS was first developed) thought it would be a good idea to market them together. That didn't work out as well as anyone had hoped, but the name stuck.
NPAPI deprecation has almost nothing to do with JavaScript. It affects Java applets because Chrome (and Firefox) implement those using an NPAPI plugin, but JavaScript is a completely different beast, and it is not implemented that way.
The effect of NPAPI's deprecation on JavaScript isn't quite zero, but it's close. The only scripts affected by NPAPI deprecation should be scripts that actually depend on NPAPI plugins to work. For example, TiddlyWiki used to depend on an NPAPI plugin to save its contents, but NPAPI deprecation prevents that, so it had to find another way to work on that browser.
It doesn't sound like you're doing anything that uses NPAPI plugins, so your scripts should be fine.