1/ Tom (Hinchcliff era.) This is everything Doctor Who should be in my opinion. It's scary, dark, not afraid topush the boundaries, isn't pandering to a stupid minority. Doesn't rely too much on past glories, but isn't afraid to use them if the story is good. (Genesis and Deadly Assassin.) It also has a wide variety of settings on alien planets, different times and features what is probably objectively the perfect Doctor. Even though I like Pertwee the best, Tom has everything the Doctor should have. He is unpredictable and dangerous, like Hartnell, Colin and even some would say Eccelston. He's funny and lovable like Troughton and Matt, and physical and capable of doing action and being a more conventional hero like Pertwee and even Tennant.
2/ Pertwee era. It ends terribly with some absolute stinkers, but overall it has a good run of stories, establishes a lot of the shows lore, has the strongest supporting characters, and one of the single best seasons overall.
3/ Troughton era. I think its first season is overrated, but even then every season has at least a few classics, and the companions this era are among the best. Jamie and Zoe are the best companion duo alongside Ian and Barbara. Also this is the only era that does the Cybermen justice. (Even Davison's time, though getting off to a great start undermines them badly with 5 Doctors where they spend the whole story getting their arses kicked by everyone.)
4/ Hartnell era. The show when it was at its most imaginative. I so wish they'd return to this style in the modern era of having a character who can literally go anywhere and was genuinely alien. Most subsequent eras tend to focus too much on contemporary earth. Even before the revival. Look at McCoy's last season. I like it, but every story is set on earth, 2 on modern day. The only thing that lets Hartnell down are the low production values and the other limitations of the time. Still it is such an ambitious, and amazing era, and has the best companions overall.
5/ McCoy era. Only counting the last two seasons. One of the best takes on the show, with supernatural elements, and some of the absolute best stories. Also Ace and 7 might be the best Doctor/Companion duo of all time.
6/ Tom (Williams) I like this era, but it doesn't quite reach the highs of the others. The good bits are really, really good, and I like the fact that they were getting away from it always being set on earth and trying out other things. Also Romana is one of the best characters in the show, who if given her own series could have been a sci fi icon as big as the Doctor. (fokk the new who crowd for not using her.) Still it does lose its steam towards the end and a lot of its big ambitious ideas aren't realised well. (The Key to Time Arc for instance. Though I like that season, the arc isn't resolved well at all.)
7/ Peter Davison. Not a bad era by any means, but as we have discussed elsewhere it lacks any clear direction. Also its lows are far worse than any of the previous eras, and it suffers from too many companions. It does have some of the shows biggest highs however.
8/ Colin Baker. I hate to have him here, but this is based entirely on his second season. I loved his first season. If we split Colin into two parts, I'd rank his first season above both Davison and Williams. His second season however drags the whole thing down.
New Who (I know it was just classic but what the hell I'm in the mood.)
Matt Smith era. I'd also rank this above Peter and Colin too. Not sure about any of the others mind, but still this is a good era. It has one of the best actors ever to play the role, an amazing companion duo, a good variety of stories, a good distinctive style, and overall a high quality of stories. (Though sadly its second season is a mess. Wedding of River Song is one of the worst stories of all time.)
David Tennant era. Not a good era of DW, but a good, fun, cheesy superhero series in its own right. Love it or hate it, it does have an important place in modern sci fi and there are a lot of good stories in their own right. It's just not really Doctor Who, or at least not a sequel to the original. It would be fine as a reimagining, but to even try to imagine Tennant as the original is silly.
Eccelston era. I can't believe this isn't at the bottom. I don't have anything nice to say about this era to be honest, other than it's not as bad as what came after.
Capaldi era. You know my feelings on this. When the show died.
Whittaker era. STOP, STOP, STOP HE'S ALREADY DEAD!