To count my time I made a little ruby script that loops into a txt file and looks for projects, calculate the hours for each and outputs them. Here is the link if you're interested : http://github.com/juliend2/compteurdetempstxt/

To invoice i use Freshbooks. I love it. But for the time tracking, i prefer my home-made solution (even if its not perfect) because i dont rely on a server so i can track my time even when offline.