Has anyone found an excellent online strategy guide for the game? Is there one that incorporates the extras added in the most common mods (missing quests, for example)?

While I don't know of any guides that include mods, DSimpson's guide on Gamefaqs is a great guide for the vanilla game, pointing you to quests, stat-raising opportunities, and where your stats are checked in conversation. The readmes for the mods occasionally have info on the quests in them, as well.

That DSimpson guide does actually include the occasional note from Qwinn, the maker of the 'fixpack' and 'unfinished business'. Not sure how much of the restored is mentioned, but game-altering bugfixes are.

It's probably the best bet for a comprehensive walkthrough.

DSimpson's walkthrough is indeed excellent.

If you're interested in a sceondary walkthrough that includes maps there's one on Sorcerer's Place :

http://www.sorcerers.net/Games/Torment/Walkthrough/toc.php

Yep, Dan Simpson is number one.
The latest version is 2.01, April 24 2009

The one on gamebanshee is pretty good, they're a good place for RPGs in general

http://www.gamebanshee.com/planescapetorment/walkthrough.php

I second that, GameBanshee is a nice website.

Yeah, but in this case their torment walkthrough is outdated, good only for the vanilla game.
If you want fixes, tweaks, unfinished business (qwinn stuff) you have only one choice: Dan Simpson.

I concur with the above posts concerning GameBanshee and the DSimpson walkthrough. I also found this guide at some place called RPG Classics. It's an ugly site, but the fact that it enumerates all your choices for a given dilemma is very nice. Doesn't seem to have been updated since 2005, though, so it likely doesn't include any restored content.

Yeah, DSimpson's Walkthrough from www.GameFAQs.com is one of the best.

Everything, like character scale changes, experience points for quests, where-to-find questions, starting character best for noobs :-), just everything (even for Qwinn mods related changes) nicely collected and segregated.