Joined: Apr 2011
The anime tended to jump to jump back and forth between multiple chapters, so I think the best chapter to start is probably chapter 35. At this point it should be at the end of her first year and moves on to the second year.
Without trying spoil things, lets just say that alot of big changes occur with Tomoko's interactions with others, mostly for the better; the comedy is still great, but I will say that the cringe levels start to lower a bit (though trust me there's still alot of that).
Currently (as of chapter 125), the manga is on her third year.