I have a 2001 S2000 with 8500 miles on it. It is a few months away from being 2 years old, it had an oil change at 5500 miles when it was a year old. The car is garaged for the majority of its life.

To keep my car in good standing for warranty work what service do I have to have performed and when? Do I go off of mileage or time?

According the maintenance schedule at 2 years you replace the air cleaner, differential oil dust & pollen filter, and of course engine oil and filter, with a bunch of Checks and Inspects. But lets face it at maybe 10,000 miles there probably isn

 

Time or mileage, WHICHEVER COMES FIRST! Plus, use a bit of common sense.
eg. - No point in changing the air filter unless it's dirty.

 

Don't know if you purchased an extended warranty or not. But that's something to consider, as the 3 year warranty is not really fair when the car has such low mileage, nonetheless, that's how it works; 3 years, 30K miles, whichever comes first.
I agree with X viper, do what is necessary and don't waste your money on "required" items that don't really need to be replaced.
If you don't have an extended warranty you don't need to worry too much about religiously following the manual's recommendations, -Change brake fluid, for instance- if it's looking good and car is garaged all the time.
With such low mileage over time, you are not likely to encounter many problems down the line, and it sounds as though you can afford a few repairs in the unlikely event that they do occur, since it's not your daily driver, it probably gets very little "wear and tear".
Just do the minimum to keep warranty valid until year 3, then do only what's absolutely necessary and don't worry, with the care you are giving this car, it will last a very, very long time.
Cheers,
Daniel