Here is a partial list of my favorite Beethoven performances listed by work category. In general the first one listed is my "reference" performance, and the following versions stand out because of some unique element - usually because they have a "revolutionary" (or otherwise transgressive) feeling...
I wish I could provide more explanations to each of my choices, perhaps when time permits. In any case, search for reviews of these recordings on Amazon, there are many great reviewers there....
Symphonies
Complete Cycles of Symphonies:
Karajan 1963
Paavo Jaarvi 2009
Leibowitz
Toscanini, NBC (1st & 2nd Cycles)
Complete HIP Cycles (Historically Informed Performance, with and without Period Instruments):
Gardiner, Immerseel, Zinman
Symphony 3 - Tilson-Thomas, Reiner, Goltz
Symphony 5 - C. Kleiber, Harnoncourt (live)
Symphony 7 - C. Kleiber
Symphony 9 - Munch, Hogwood, Furtwangler 1942
String Quartets
Takacs, Endellion, Guarneri
Piano Sonatas
Gulda (2nd cycle), Richter (incomplete), Annie Fischer, Paul Badura-Skoda (HIP)
(for this category I did write a post with more details HERE)
Diabelli Variations - Gulda, Richter (Prague),Puppulo, Katchen
Concertos
Piano Concertis:
1-6 - Schoonderwoerd/Cristofori
1 - Argerich/Ozawa, Aimard/COE, Richter/Munch
2 - Argerich
3 - Richter/Bakala, Aimard/COE, Annie Fischer/Fricsay
4 - Katchen/Gamba
5 - Katchen/Gamba, Gulda
6 (VC arr) - Barenboim
Choral Fantasia - Brendel/Boettcher, Grimaud, Richter/Sanderling
Violin Cto - Heifetz/Munch, Kopatchinskaja/Herreweghe, J.Fischer/Zinman
Triple Cto - Richter, Oistrakh, Rostropovich, Karajan
Haitink/COE
Badura-Skoda/Maier/Bylsma (HIP)
Chamber
Violin Sonatas - Kremer/Argerich, Heifetz, Oistrakh/Richter, Szigeti/Bartok
Cello Sonatas - Maisky/Argerich, Rostropovich/Richter
Choral
Mass in C - Gardiner, Nanut
Missa Solemnis - Bohm, Herreweghe
Overtures
Zinman, Karajan, Munch, Toscanini, Dorati
Again this only a partial list, lots of favs are not here (most notably Bernstein, Abbado, Budapest Qrtt, etc...)...but if you have all of the above you should be pretty happy!
