The only issue I had was that it breaks W3C validation. The code produced by the module/plugins is not valid - my homepage was valid until the Shopping Cart was shown, then it failed by 16 errors (mainly due to unclosed tags and none-escaped ampersands). Not a huge issue, but one that was enough for me to look at and implement an alternative solution.
Yep, it's just about the answer to anything you need customized in your site. The more I use it myself, the more new ways I find to use it.