Call me naive, but if Google says they're not sneaking private info off your machine, that's good enough for me.
I used to use Scopeware Vision (a great tool, but the company busted). One day after installing the Google Desktop, I uninstalled Vision and never looked back.
I don't store my email in multiple folders based on some arbitrary relevancy. I have 2 folders for 5Gb (slightly over 50k messages): Inbox and Read. Any time I need ot look something up, I use the desktop interface (10s of times per day).
Google desktop is blazingly fast. I'd even pay for it if I had to.