I would do the Dark Brotherhood, Thieves Guild and most of the Daedric quests first. I think the only really "good" Daedric quest is Meridia's Beacon. And maybe Sanguine Rose (A Night to Remember) and Wabbajack are more silly than good or evil. Azura's Star is only good if you choose to work with Aranea Ienith to cleanse the star, rather than taking it to Nelacar to make it evil. Some of the Daedric quests have options to choose a good ending -- like sparing Brother Verulus and killing the Namira cannibals instead, or sparing Erandur during Waking Nightmare -- but you won't get the Daedric items.
If you have the Dawnguard DLC, it isn't possible to join both the Dawnguard and the Volkihar Vampires in the same playthrough -- you can only be one or the other, and you can't switch sides once you've chosen (though you can later cure yourself of vampirism, if you desire). So you might want to be a vampire and get that out of the way, or you might want to avoid the questline until you're ready for redemption, and then join the Dawnguard.
The Companions are a bit morally dubious, imo, because they become werewolves and people generally don't like werewolves. But it is possible to cure Kodlak, Vilkas, Farkas and yourself, for redemption at the end of the questline. My first character cured everyone, including herself, and then killed Aela because Aela refused to be cured of the beast blood.
There are some malicious side quests, like Lights Out in Solitude, but they're not that important. You can either do them early on, or just ignore them later when you are "redeemed."
I would save the Dragonborn DLC for when you're redeemed, maybe, since you'd be driving Miraak out of Solstheim for the benefit of all. And I would put off the main questline for awhile. Just don't take the dragonstone to Farengar, then whenever you're ready to "find your destiny" as the hero who saves the world from Alduin, go ahead and do it.
I don't think the College of Winterhold or the Bard's College questlines are particularly good or evil, they're just about knowledge, which can be used either way. Though, in Winterhold you have to basically save the world from the power of the orb and the tyranny of the Thalmor trying to use it, so that one might fall into the "good" category.
Anything where you have to help people -- restoring the White Phial, Book of Love, fetching a sword or book for someone, etc -- might want to wait until you become a good person.
See a list of all quests here: http://elderscrolls.wikia.com/wiki/Quests_%28Skyrim%29