First saw it when I got my first job at a video rental spot after high school (which allowed me to plow through the classics pretty quickly) and my first impression was that it completely shattered my perception of what a western was supposed to be. My dad was a fan of the film and recommended it to me but I'd been wary because he was also a big fan of classic westerns starring John Wayne and had showed some of them to me when I was younger and I always hated them. So "El Topo" was one of those game changers for me- the "Trout Mask Replica" of westerns if you will.
Later when I rewatched the film and started turning friends onto it, I started to really appreciate the satire, black humor and symbolism. Jodorowsky really seems determined to cram as much symbol-rich imagery into every frame (there's a book version where he analyzes everything- own it and will read it at some point but I'm kinda concerned about it being "ruined").
Within the last year or so I got to see it on the big screen for the first time (at the Roxie here in SF) and it was the greatest filmgoing experience of my life. Went w/ 2 of my closest friends (who are also Jodorowsky fans- important distinction) and the audience loved it and responded enthusiastically yet appropriately (loved the fact that the Russian roulette in the church scene got a huge laugh).
Objectively, it's not a perfect film. The acting and some aspects of the production are a bit amateurish and dated. I mean, it was an underground film and has the distinction of being credited with creating the "midnight movie" phenomenon. That fact and its list of hip fans like John Lennon (an early supporter, which led to ABKCO providing initial US distribution), David Lynch, Bob Dylan and Peter Gabriel (who cited it as an influence on "Lamb Lies Down") definitely help add to the film's mystique. But the bottom line is I've never seen anything quite like it (including Jodorowsky's other films) and I never get tired of it.