- Pay attention to error return codes when writing values, and make sure that the data you wanted to write actually gets written. Read it back after the write and checking for a correct value.
- It takes a while to write to data. If your EEPROM supports a "finished" signal, use that instead of a fixed timeout that might or might not be long enough.
- Don't access the EEPROM with marginal voltage. It is common for an external EEPROM chip to need a higher minimum voltage than your microcontroller. That means the microcontroller can be running happily while the EEPROM doesn't have enough voltage to operate properly, causing corrupted writes. In other words, you might have to set your brownout protection at a higher voltage than normal to protect EEPROM operation.
- Have a plan for power loss during a write cycle. Will your hold-up cap keep things afloat long enough to finish the write? Do you re-initialize the EEPROM when the CPU powers up in case the EEPROM was left half-way through a write cycle when the CPU was reset?
- Don't use address zero of the EEPROM. It is common for corruption problems to hit address zero, which can be the default address pointed to in the EEPROM if that chip is reset or otherwise has a problem during a write cycle.
- Watch out for wearout. EEPROM can only be written a finite number of times. Make sure you stay well within the wearout rating for your EEPROM.
- Consider using error coding such as a CRC protection for critical data items or blocks of data items stored in the EEPROM. Make sure the CRC isn't re-written so often that it causes EEPROM wearout.
You might also be interested in my blog post on EEPROM and flash memory wearout.