I have first watched the anime then i found out about the manga somewhere around the Inubushi Castle case.
I would say that from Episode 1-345 is the best for me, it had a lot of great/good gosho and AO cases. There have been some misses here and there but this is my favorite "part" of DC.
After 345 till the intro of Kir 425 i would have to say that there are some great/good cases here, granted some are torture to watch, and dont have much complain here. I almost forgot to say that in this part of DC Kid started to suck
From 426-504 cases were like...good, then bad, then good, then bad
If you were to take the best out of the AO and skip the bad ones then its a great story, then again Gosho had his fair share of bad to me in this one. I liked eisukes intro in this part, and thought there was not enough of him. The Clash series is Phenomenal.
From 505-666 it was, some are good some are that i don't care for and why even make them, the AOs became a drag much like goshos cases. Granted there are the Shiragami case, the guardian of time, inubushi castle, red wall and the mansion of death exceptions. I did not like holmes revelation. This part was bad.
666-766+manga
So many bad filler cases, so much bad AOs, Amuro didn't impress me, later i decided that Sera was pointless in this arc.
I love train cases, add the BO to it and i should have one of my fave cases ever...yet i was somewhat disappointed.
THere are a few nice ones like kogoro in the bar and makoto vs kid and heiji and the vampire mansion, and i love Dancing Demon at the Noh Mask Mansion.
The way bourbon arc ended was a disappointment. Spying and having a car chase while watching an award show...no
After that showdown there have been some interesting case in the manga by gosho