The only time I use GA is for one particular client, and I embed the GA code directly into the theme footer.
For favicons, my theme framework has built-in support for this, so if the client wants it, all they have to do is drop an appropriately-name image into the theme's image folder and it works with no further work needed.
For meta tags, I have a custom function I wrote for my theme framework that handles this. It builds the tags based on either the contents of custom fields on each post/page, or post tags (for keywords) and the post/page content or excerpt (for the description) with defaults assigned through the theme options page. I uploaded an edited version (to work without my theme framework as a plugin) here.