I found info to replace /System/Library/SystemConfiguration/mobilewatchdog.bundle/ with "mobilewatchdog" from iOS 3.1.2 (you can use iExplore to navigate to the iPhone).
But that seems to only work on iOS 4. Since i have iOS 5, i searched some more and found this solution where /System/Library/Watchdog/MemoryMonitor.bundle is deleted and mobilewatchdog is copied in.
Update apr 2012: i found this solution for reboots on iOS 5.
Update: Since the problem occurs a little random, i don't know how soon i will know whether it works or not :-). But i already had 2 new reboots after doing the above :-). So i think this did not work for me :-). I did a 'install as new iPhone' after which i restored the backup of my iPhone, but within a day, it started rebooting again :-(. So since Dec 30th i did a 'install as new iPhone' again, but without restoring the backup, installing only the apps i REALLY want, and see how that works... As i'm writing this i've already been withour reboots for a couple of days...
Update: decided to try and downgrade to 4.3.5 and see whether the mentioned edit of the mobileWatchDog will prevent my 3GS from rebooting by itself. Found i needed this to edit the hosts-file (as Apple does not allow downgrading) and will try this to still be connected to the devices in my family that are synching with iCloud.
Update: after restore the iPhone would not connect to the network anymore. Tried everything, carrier fix, new carrier settings, new unlock through iTunes ... Nothing.
After all the 'install as new' and new jailbreaking, i had problems with iMessage: that would not deliver the messages anymore. Also, i would not get WhatsApp push messages. Found this page, and SAM/SAMPrefs solved that problem!
I have also tried the delete-all-email-accounts-and-add-them-again-trick, but that didn't work either. Just tried saadalsakran suggestion. I also just learned you should check out the log under Settings/General/Info/Diagnose&Use: after my last crash i checked and it showed a 'LowBatteryLog-
Imagesource: sudgaurav's blog.