Ranking the ones I can be assed to remember. (my favorites)
1. 5 and 6 "Girl A" arc ~ It's a pretty cute little arc that does the sort of humor I think works best for Kamen Rider. I usually don't like kid centric episodes, but I think the story behind this one works nicely and as much as I'd have liked Asuka to learn the truth, I'm glad she didn't, a kid that adorable crying would be torture.

It also did a lot for Shotaro's character and made him much more interesting to me...too bad that after this, the only episodes I liked until Terui came in were the Virus and Sweets ones.
2. 42 and 44 "Old" arc ~ Probably the strongest written episodes of the series in that they do a lot to make the thing seem like one cohesive plot and not just an ass random series of events. We see that Shroud has been behind just about all of the events, from Skull, to the birth of Double, to Isaka and Terui. I had a great moment of realization at just how well written this series could be because of these episodes. I also love that it shows how much Terui has grown as a character, the fact that he forgives Shroud for what happened does a lot to show the maturity of the writing. I kinda didn't like what it did to Shotaro at first because it emphasized the points I dislike about his character, but in the end I saw it as an arc that shows what Shotaro means to the others.
3. 35 and 36 "Beyond R" arc ~ Mostly because it closes up Ryu's story with Isaka, we see him get revenge, but at the same time, we see him becoming more of a hero in the general sense and not just when it deals with his past. I always like training for new power ups, so that was a definite plus for me.
Those are my favorites and after those I am pretty much a fan of anything after Terui comes in...except for that nasty Liar arc, the one bright spot there was the creative use of attacks in that Dopant. Annnd Gene was particularly amusing to me for its movie setting and that cow puppet hand moment.