Picking the perfect Beethoven set is hard!
If you want a complete cycle, my personal favorite has always been the 1962 Von Karajan Set.

People will bitch about it because it is a bit hissy. This is true but it's also a good sign that the tapes weren't no-noised. I have heard rumors that there are better tapes of this cycle but I have yet to hear them or even know of a commercial release using the better tapes.
My next favorite is this set:

Gardiner did a fantastic job with this cycle. I believe he used period instruments. The sound quality - stock - is superb and you can pull A LOT out of this set using a good EQ.
Now...as far as individual performances go...
This is one is just superb...

Benjamin Zander is not only a conductor and pianist but a great musicologist and researcher. He went in-depth when studying Beethoven's works and noticed that most, if not all performances, were done at the wrong tempo. Further research led to this performance and the result is nothing short of exhilarating and great. Hearing the correct tempi for these symphonies is an eye and ear opener. This is definitely my favorite performance of the 5th and 7th. Sound quality is superb.
Here is a small sample but trust me - the recording is much better.

Ditto on the above except for the 9th. Probably the most glorious 9th I have heard. I really wish Zander would do the entire cycle. He definitely has a special touch with classical music. Here is a TED TALK he did...
Hope that helps out a little bit. I have a ton of Beethoven and these are my favorites.