Try starting in Safe Mode and remove the "runaway app". To start up into Safe Mode (to Safe Boot), do this: 1. Be sure the computer is shut down. 2. Press the power button. 3. Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone but not before. 4. Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear). During startup in Mac OS X v10.4 or later, you will see "Safe Boot" on the login window, which appears even if you normally log in automatically. During startup in Mac OS X v10.2 through v10.3.9, you will see "Safe Boot" on the Mac OS X startup screen. To leave Safe Mode in any version of Mac OS X, restart the computer normally, without holding any keys during startup.
Try resetting the PRAM (this resets the power management part of any Mac). turn off the computer, press the power button and as soon as you hear the startup noise press and hold Command + Option + P + R. The computer should turn on, light up and then turn off, KEEP HOLDING the keys until you hear the startup sound for the SECOND time. =)
Try starting up the computer in Verbose mode. Shut off the computer if it's on, press the power button, and hold Command+V . Verbose mode will show (in text) everything the Macbook is doing while booting up. If it stops at one point or starts saying something over and over in an endless loop, please post it here =)
On most laptops newer than 2005 (almost all) the cmos battery was replaced by a capacitor instead. As far as I know, the capacitor cannot be replaced or even disconnected easily. And sadly, the capacitor can usually hold a charge long enough to last the lifespan of the computer.