i simply based it on my previous portable's usage. my 15" MBP has a 500GB HDD, of which i consumed almost half at the time i ordered the 13" MBA. to future-proof it as much as possible, i went for the 4GB option. once i sifted through my MBP for only what i needed, i still had over 128GB of data that required me to get the 256GB version.
since i needed the 256GB MBA, i decided at that point just to throw in the 2.13GHz CPU upgrade anyways. my biggest fear of cheapening out and getting the 128GB was waiting for a cheaper aftermarket solution to upgrade the internal storage.
basically, just look at your current needs and use that as a guideline. if you're within 20% of the maximum, it'd be wise to step up to the next larger size if possible. an external HDD is a solution, but it's an inconvenient one especially if you've bought the MBA specifically to reduce the amount of stuff to carry.
there is also the USB flash drive option since there are 128 and 256GB USB drives that can more elegantly expand your storage space if cargo space is a concern.
but generally the question youve asked is one that only you can answer.