For one-offs...
This,
this, and
this, plus Charlie Brown and the Butcher's Diagram that that other guy listed.
As far as stuff from within story arcs, here's my top five, in chronological order, since I couldn't decide how to rank them. Honorable mention goes to basically every strip from the Cartilage Head arc, which all probably could have made it onto the list if I'd made it longer. I feel like I have more to say about these strips anyway, though:
Nov. 18 2003 - "Omega Tetris" Please tell me I'm not the only one who has actual anxiety dreams about video games where shit like this happens. I don't know what it's like to search frantically for a kidnapped child, but I'd venture to say it's a completely analogous feeling to that. More intense, certainly, but still fundamentally the same. I thought the Ardbeg tetrad looked more intimidating, but I had to go with this one one the merit of the other four panels. Omega Tetris,
and Lyle ribbing Cornelius about doilies. Splendid.
Jun. 9, 2004 - "Success!" A terrific ending to the Uncle Culpepper arc, which then segued into almost a full week of gratuitous ***** ass-nudity. Lie Bot's ass makes its triumphant return, the artwork is beautiful, and the whole sequence just rubs in the fact the the entire arc had just been a practical joke by the 'Bots. WHOOO!
Feb. 4, 2005 - "Scenes from a party" If I ever buy a signed copy of a strip, I'm gonna get a triptych with this one and the two preceding strips. Not as popular as Ray getting stoned, I'm sure, but I think this one best captures the spirit of Achewood's party arcs.
The Tenmen are playing live from inside Ray's bathtub. It doesn't get better than that. "Maybe go home before piano fall on you" is also a gem, and the last panel is totally me at a party I went to with my parents when I was Philippe's age... but that may be a story for another time, I think.
Apr. 11, 2006 - "Philippe's creekbed bedside" A perfect juxtaposition of the Two Achewoods: Witty dialogue, character-based humor... sandwiched between the kind of creepiness and foreboding that marks Achewood's darker side. Side by side, each only adds to the appeal of the other. The arc as a whole is also one of my favorites; it's even more amazing when you realize there was only a single strip between this and the GOF.
Sep. 29, 2006 - "The helicopter sprouts legs" Yeah, Ray, don't Flintstone that bitch! Also, one of the most surreal Achewoods ever. The second strip following this one is also great, as it basically drops Ray and Bensington straight into
The Saragossa Manuscript, but I remember being disappointed at the time that it reintroduced words to what had become a silent arc.