For me, it is symphony #3. My second favorite is #1. In fact, these are the only two Beethoven symphonies I listed to on a regular basis. Least favorite is the eighth.
Eh, the 3rd is my least favorite. I find it relatively long-winded and tedious. (Though maybe I just haven’t heard the right version).
I really like the 8th. It’s the fun one. Though I would never argue that it’s better than #5, 6, or 9.
The best version of the third is the Roger Norrington cd. I’ve had the recording for close to 20 years.
Depends on mood, exposure, recording, live experience. The 9th is great, Furtwangler’s 1951 recording a masterpiece, but who could listen to it every day? Same goes for the 5th with Carlos Kleiber; Bohm’s 6th is the most faceted one and Klemperer’s Eroica is just stunning, but, like all the other ones, you have to be in the mood.
Beethoven live can be a marvelous experience, his music is so tactile that it is a whole-body experience; and as long as the orchestra gets the tempo right, the rhythmic pulse of each movement and their tempo relationship towards each other, I usually enjoy the performance even if they do not stand up to the masterpieces.
The only symphonies I rarely listen to, are the 2nd and the 1st; but they are interesting in their own right, because they show a Beethoven who was still awed by Haydn and Mozart and had yet to find himself.
Anyway, as genius as Beethoven’s symphonies are, I enjoy Schubert more.
Yeah, a divertimento. But fun. (Well, the “but” doesn’t make much sense, “but” you know what I mean)
My favourite is the 7th, but I love them all dearly. 3rd, 5th, 6th, 8th, 9th, 1st, 2nd, 4th - can’t go for a month without hearing at least one of the once.
Ninth is the best overall, though I’d put the 7th just slightly behind it.
Another vote for the 7th.
I like the 5th because I associate it with WWII, an interest of mine. The four opening notes sound like Morse code for ‘V’, which is for ‘victory’. It conjures images of B-17s and Lancasters and B-24s and Mosquitoes. I saw a video that had gun camera footage of a P-47 on a long strafing run, the one long note at the end of a phrase stretching out with the tracers. The Fifth just resonates for me.
I like the 7th the best, because you don’t hear it as often, and because it is so classically classical.
The 5th and 9th and 3rd and 6th and “10th” are close behind.
I love 5. I love the last movement, which you don’t usually hear on “pops” classical radio. 7 is pretty good, especially the third movement. 3, of course. And 9, but you have to fast forward to get to the good part. 
My favorite part of the fifth is the slow movement, which for me always conjures up images of a bunch of Germans in a tavern swinging big steins of beer! 
My favorite is the 7th.
Edit: Or the 3rd. Or both.
If I must pick one, it’s the 7th . . . especially the 2nd movement.
9th. Completely epic from beginning to end.
Every one but the 6th?
I have versions by Bernstein (I finally got the 8th last week.) For me it is probably the 9th, than the 5th, (especially the last movement) then the 4th (one version I have has amazing violin work there, totally toned down in another.) The version of the 8th I had before was mediocre, so I suspect that this will start rising. And the 7th, and the 3rd, of course. Eh, like I said on the first line.
Schubert does come in second as far as symphonies go.
My favorite is the one I’m performing.
Oh by the way, here’s a recommendation for you all for a complete set:
Beethoven Symphonies 1-9
Berlin PO, Claudio Abbado
DVD
$31.49.
A fantastic set–stunning, energetic performances–at an amazing price.
I like the 4th. Or maybe I just like the allegretto - I can’t remember what the rest of it sounds like
In order from favorite to least favorite:
5
7
9
6
1
3
8
4
2
The 7th is usually paced too slow. I had a great recording years ago by Steinberg and the Pittsburgh Symphony, but it seems to be unavailable now.
#1: 9th.
#2: 6th. I freely admit this is heavily influenced by Fantasia (and a kids’ 45 of The Lonesome Pine).
Least favorite: 5th. It just doesn’t do it for me any more.