I'm a "power and speed" kinda guy, so it won't come as any surprise that most of my Furtwangler choices are performances with the Berlin rather than with Vienna. And I often tend toward the drive (near-mania?) of the wartime stuff versus the smoother and more contemplative approach of the years just before his death.
His 1942 Beethoven 9th (the famous March version, not the April "Hitler's birthday" performance) still astounds in the emotional response it elicits and the power it expresses. The 1944 Bruckner 9th, as already noted, offers similar qualities. The Beethoven Eroica of Dec. 8, 1952 is a great one. In concerti, the early '50s Emperor concerto with E. Fischer is more straightforward, with far lower emotional amplitude than some of my choices, but it's a wonderfully fulfilling presentation of the music IMO. And the Beethoven violin concerto with Rohr is very special. Furtwangler's takes on the Schubert 9th--wartime and early '50s versions--are quite different but both compelling. Beyond these, much of his wartime and early postwar Brahms could be added to my list. So would what little Schumann he left us. Wouldn't want to be without any of these.
Dirk