Here are some picks from various sources including Physics World:
Daniel Kleppner : Hydrogen Maser
Perlmutter and Schmidt: Increasing expansion rate of the universe and hence dark energy postulate
Guth and Linde: Inflationary scenario
Berry and Aharanov: Aharanov-Bohm effect and also the related Berry phase
Pendry and Smith: Negative refraction
Penrose, Hawking: various developments in General Relativity and Cosmology
Suzuki (Super-K) and Macdonald (SNO): neutrino oscillations
Unfortunately the Guth-Linde inflationary picture is not yet completely confirmed experimentally, and Penrose and Hawking do not have any specific prediction tested by experiment which is what the Swedish Academy looks for in theory prizes.
Do put in your nominations — even though the Swedish Academy is probably not one of the regular readers of this blog 
