Here's my list. It's a top 10 list, with more explanation than is probably necessary, but that's just me being detailed (I'm bad at being concise). I have yet to see about eight of the episodes, so this may be edited at a later date.
10. "TAKEAWAY" - The camera angle when the sheep tower/scarecrow takes its first steps is impressive. Also, Santa Lucia is one of my favorite tunes (it's in the background towards the end).
9. "THE KITE" - The first time you see this is the best, especially since you aren't expecting Shaun to rocket through the tree right next to his target like he does. Bitzer's also pretty good with the drums!
8 ."WHISTLEBLOWER" - The sheep and pigs' reaction to Bitzer's first "fanfare" is pricless- small wonder it went to his head!
7. "THE VISITOR" - Got to love the Basil Fawlty reference with the tree branch!
6. "COCKADOODLE SHAUN" - The unusual plotline and the new scenery for the countryside outside the farm make this one even more enjoyable than most (and, to be frank, Bitzer makes a pretty silly chicken!)
5."EWE'VE BEEN FRAMED" - I have to say, I have seldom seen anyone laugh so hard as my dad when he saw the part with the cow and the tractor, and later the incident with the scarecrow.
4."CAT GOT YOUR BRAIN" - As far as skill in bringing characters to life and giving them personality goes, this one blew me away; switching two diametrically opposed personalities like that is a good way to show off clay-mation at its best.
3. "HICCUPS" - Shaun plus pitchfork plus inflated fertilizer bag....what could possibly go wrong?
2. "THE MAGPIE" - The farmer's role in this one was so hilarious, and there were several other elements (Bitzer's whistle being swiped mid-blow, Shaun becoming magnetized, etc.) that for a long time made this one my absolute favorite, until I saw...
1. "TWO'S COMPANY" - This was the first episode that made me genuinely cry; when Bitzer got Lola and Shaun back together I lost it (I'm a big softie). There isn't as much humor in this one as some of the others - though in places it is really funny - but what makes this one for me is the storytelling. Never in my life have I seen as good a job of making engaging and even heart-touching stories as Aardman does with some of their movies on a regular basis; to be able to pull that off with no spoken dialogue and such silly characters as semi-intelligent sheep, militant dogs, and nearsighted farmers made of plasticine is, to me, extraordinary in the extreme!