How are you using Custom Fields?
We use custom fields for notes that don't fit in a description field for payment distributions or when there are some additional information information to note on invoices or vendor records that don't typically fit in other areas of the record.
On invoices we use attributes to track expenses associated with a giving campaign or gift officer. We use one of the Transaction Codes (General Ledger > Configuration) for tracking expenses/revenue associated with Raisers Edge Events/Appeals.
We have a job number for our Weatherization jobs so they can pull all expenses for a single job by filtering on that custom field.
We are also considering using this in the same way with a client ID# so we can access what sort of support we have provided each customer.
We also have a custom field in the Grants module for a signed date. So our CFO can pull all new contracts/grants based on the signed date.