OMG, how can I choose only one.............
OK best overall modern instrument performance/value/sound goes to:
Zinman/Arte Nova
How can you beat that price, I like this a bit better than the 1960 Karajan/DG warhorse, these modern instrument performances have the benefit of learning from various period performance sets of the previous 15 years, produces generally faster tempos and clarified textures........this is a no brainer. (also have the MacKerras/EMI set mentioned above, but like the Zinman a bit better......tempos are a bit faster)
If money is no object I guess my very favorite modern instrument performance is:
Abbado/DG (2000)
This set completely eclipses Abbado's ponderous 1980's DG set with VPO...............Abbado was greatly influenced by period instrument movement and using modern instruments the style is dramatically transformed from 1980's set. the sound is excellent and packaging is the best I have seen for any Beethoven set.
Finally everyone should own a period instrument set and the best overall for me is:
Gardiner/Archiv
Actually the pioneers in this movement are Norrington and Hogwood, I have both of these sets also. Gardiner's set came several years later and he learned well from others creating a set that has the best ideas/styles combined. Sound is not great but very good.
BTW.........I saw in latest Penguin guide they really like new Rattle/EMI set at mid price, but I have not heard this set myself.
(I will probably purchase it sometime soon)