When DS was in the NICU, the hospital gave us a binder to keep all his info -- test results, vaccinations, medications, milestones, etc. but never kept it up to date. I used to keep a notebook, then graduated to a dry erase board in the kitchen to check off meds given, times, amounts eaten (formula)...
I keep a spreadsheet of all his meds, amounts, times per day taken, when tobi started or ended... And at the bottom keep an ongoing list of questions for the doctor to ask at future appointments. I print it out prior to appointments.
As for medical records, since our local cf clinic is less than forthright about culture, lab results, etc., I always fill out a release of information form after an appointment which includes everything, including doctor's notes. These I send onto his primary CF doctor in the City and keep a copy in our filing cabinet.
If I need to check information about growth percentiles, when he got sick last, cough that developed... I always seem to mention it in his blog, so I can look back at that and see how he's tracking or if there's a correlation between symptoms and say starting tobi, weather changes...
A computer program to keep track of all this would be great, 'cuz I tend to type better/faster than I write.