This is a very hard one. Metallica was the band that got me into metal and I know I'm not alone on that. I too LOVE Battery because it's so brutal. The flamenco style intro is very deceiving, and when the distortion sets in its a 4 minute panic attack until the end.
One is one of my favorite songs of all time. I never thought it could be better, but they did an AMAZING job on the S&M CD. If only one song worked with the orchestra, it was definitely One. The clean intro, the solos, the machine gun riffs near the end...the song is just amazing. This is Metallica in its best songwriting phase. By far the best epic metal song ever.
Kill Em All was still a good CD, but Metallica hadn't found their complete sound. I loved The Four Horsemen, Seek and Destroy, Cliff's bass solo, and Metal Militia, but I definitely wouldnt say that any of these songs are their best. Seek and Destroy is awesome for cruising around on a Saturday night though.
On Ride the Lightning I think they really got into their groove. The Ride the Lightning song is pure chaos and contains some of the best Kirk Hammett solos IMO. Everything about Fade to Black is amazing. I have fond memories of seeing them in concert, and saving our joint until this song came on. For Whom the Bells tolls is another great song for when you just want to rock out. They did real good with all of their war songs.
Master of Puppets has got to be one of the most recognizable songs in metal. This was my favorite CD...every single song on MoP is amazing. The intro was one of the first riffs I learned how to play, and I sounded like **** but looked cool doing it. This is one of those songs thats pretty long (around 8:30 or 9:00 IIRC) but it doesnt feel like it. It has such a great rhythm and feel to it that it still seems to end too soon.
Everything started to go downhill on Black. It was still a good album, but they started to change who they are. Track lengths dropped, as did the overall complexity and speed of the songs. The Unforgiven and Wherever I May Roam were two astounding songs on an otherwise average album. Yes, the rest of the tracks were OK, but nothing stood out like most other tracks on previous albums.
Everything after Black pretty much sucks balls. There's no getting around that. Garage INC was cool for the B-sides and covers, and S&M was good for the added effect of the orchestra, but Load and Reload were complete garbage.
As for the question at hand...if I could pick a few it would be One, Fade to Black, Sanitarium, Harvester of Sorrow, and Master of Puppets.
I guess if I HAD to pick one, I'd go with Fade to Black. I LOVE that song. The intro is the first solo I ever learned. I still play it every day. The song is just amazing. Metallica has had many good songs though, I didnt even list half of them in this monstrosity of a post.
EDIT: Here's me playing that Fade to Black solo if you haven't seen it. Still not perfect, but I'm a lot better than I used to be
http://youtube.com/watch?v=rkwr_UnYWOU