1. Make sure at least 10% of your HDD is free. Ideally 10gb if your drive is so small that 10% is less than 10 gb.
2. Repair Permissions (in Disk Utility, select your hard drive and click Repair Permissions).
3. Check to see what's in your login items list. Go into 'Accounts', and then with your user selected, see what's in the LOGIN ITEMS list. Try to keep a maximum of 3 items in there. If anything looks suspicious, or you don't know what it's for, remove it.
4. Back up everything & re-install OS X if none of the above work.
5. If none of the above work, either the hard drive or RAM are faulty. It's also entirely possible the Logic Board has had it (would explain the clock issue), which is a pain.
When I say back up everything, I mean EVERYTHING. Get an external HDD, and take a disk image of the hard drive. Slow performance/kernel panics/certain features not working are a sign of impending hard drive failure. The more you stress a hard drive, the closer it will come to failing, which is why I recommend you back everything up before doing any serious work with it (such as re-installing OS X, which doesn't necessarily mean losing all your work).
Good luck, and keep us posted!