Generic tire repair "strings" to plug holes, and a Cycle Pump
from Aerostich. The Cycle Pump seems absurdly expensive (it was "only" $80 when I bought it), but I have had mine for 10 years, and it still works. I replace the tire repair strings and goo each spring. Everything, including the OEM tools, and a secondary tool pouch, fits under the seat of my 1999 R1100RT.
That said, the two flats I have had in the past 60,000 miles were both unrepairable. The first was a large roofing nail, which required 2 or 3 strings to hold enough air to make it to a dealer 15 miles away, stopping every 5 miles to pump up the tire. The second, on Skyline Drive, in VA, involved hitting a chunk of oak the size of my thumb that penetrated 2 steel belts, leaving a large hole in the tread. After a tow to Harrisonburg, VA, Anton Largiader of Charlottesville graciously fitted a new rear tire on short notice, and I was on my way.