Without knowing what you've tried, try these: (though first, remove any unnecessary USB or FireWire devices... that means only have your keyboard and mouse connected.)
OptionA) Reboot/reset/turn-on and hold down the shift key. If the machine is trying to boot into OS-9, then this will disable the extensions. Keep the shift key depressed until the screen says something to the order of "Starting up, Extensions Off". Wait for the OS to finish booting and go to the control panel to change startup.
OptionB) Reboot/reset/turn-on the computer. Immediately after the startup "chime", hold down the [Command]+[Option]+[P]+[R] keys, and KEEP THEM HELD DOWN until the chime tolls 3 more times. (Depending on the amount of RAM and other options, this could take a while, but shouldn't be more than a minute or so.) You have now reset your "P-RAM" and depending on the specific model, the computer may prefer OS-X as it's Parameter default.
OptionC) More dangerous: Turn off the computer and remove the power cord(s) from the back. Open up the side panel and look at the mother board. You're looking for a small (1/4in / 5mm) silver, square component with a circular button on it.
Push this button and RELEASE IMMEDIATELY! DO NOT hold the button down! (Holding the button down for more than half of a second WILL fry your motherboard.)
You have now Reset the motherboard to factory defaults, again, hopefully it will prefer OS-X to OS-9.
OptionD) Safest, but requires a purchase. Pick up Norton SystemWorks for Mac. The CD is bootable, and will let you do disk maintainance (data errors, optimization, etc.) AND has the same "Startup-disk" controls built in.
Once you have booted into OS-X, go to the "Classic" control panel, and in the Advanced tab, click "Rebuild Desktop". This is the same as holding the [Command]+[Option] keys at OS-9 startup. (If you haven't been rebuilding your desktop, this could account for at least part of the problem you're experiencing.
I would suggest migrating to OS-X anyway, and run any OS-9 applications in classic mode. (Yes, I too had my doubts, but I have seen the light.)