I too have been perceiving some reduced battery performance on my 3GS. Got it Sunday and it just seems that it was getting lower faster. I typically had most services on (wi-fi, Bluetooth, 3G, Notifications, and sometimes Location Services). But, I quickly turned off location services since I rarely use it at this point.
So, as a test, I charged my phone fully overnight Tuesday to Wednesday. Turned OFF 3G, Bluetooth and Notifications (Location had already been off for awhile. Then took it of the charger at 7:30 AM EST. It is now over 26 hours later and I have 54% battery left with no charging since I removed it yesterday (Wednesday). Wi-fi is on and actively used. I have used it for multiple short phone calls, quite a bit of web browsing, watched a short video I had shot, used Stanza for 30 minutes, manually checked email multiple times, about 10 texts, 2 games of checkers, several sessions with the game Paper Toss, checking Facebook quite a bit, checked weatherbug, used the alarm clock to wake up today, 3 reboots, 30 minutes of playing music via the iPod app, app store checks, etc..... In essence a normal usage day - without watching heavy videos which I sometimes do.
So, I am obviously seeing something here. My usage (except for less video) was very normal for me. I use the iPhone a lot. Between shutting off 3G, Bluetooth and Notifications - the battery performance now seems to be spectacular.
I am going to let this thing go all day today to see how far I get. I will charge overnight tonight and add 3G back in. I want to test services one at a time to see what the worst offender is and what I can live without. I am hoping the issue is Notifications, which is not a huge deal for me. Would be nice, but not worth horrible performance. I'll post something more when I get more results.