I found a very nice list of hard-to-find quests in WoW right here, but I decided it could use a face lift. So I reformatted it into a much more usable guide. Currently this is for Alliance only (though a few of the quests can be done by Horde).
The list itself belongs to the original poster.

Kalimdor Eastern Kingdoms
Teldrassil
Darkshore
Ashenvale
Stonetalon Mountains
Desolace
Barrens
Dustwallow Marsh
Thousand Needles
Feralas
Un'goro
Azshara
Silithus
Tanaris

Teldrassil

Mist
Find this cat to escort at the back of one of the harpy camps.

Darkshore

One Shot, One Kill
In the hills in the far south of Darkshore. (NOTE: the time between waves is REALLY long (like two minutes) and you have to wait a minute after killing the named mob before getting credit. Just be patient.

Ashenvale

The Howling Vale
This long questline that starts in Ashenvale leads to Darkshire and explains the Worgen there.

Stonetalon Mountains

Ziz Fizzik's quests
In a hut SW of Windshear Crag

Gerenzo's Orders
Off the road, above Ziz Fizzik's hut

Desolace

Claim Rackmore's Treasure!
Starts at a book among some wreckage on the shore, next to a chest for an Alliance quest

Azore Aldamort's quests
Just north of tower overlooking the ocean. Aside from 1 BFD quest, the only Argent Dawn rep before level 50.

Gizelton Caravan
This is a quest to escort a caravan along the road. You can do this quest 3 times at 3 different spots along the road. His bots (http://thottbot.com/?n=94036 http://thottbot.com/?n=95337) also sell some hard to find recipes between escorts.

Galen's Escape
He is in a cage on the east side of the hostile Draenai camp.

Get Me Out of Here!
She is in a basket next to a tent in north part of Maraudon camp.

Ghost-o-plasm Round Up
Good to do while doing the SM prep quest.

The Pariahs Instructions
He wanders south of Mannoroc Coven.

Shadowshard Fragments
Starts at the top of the tower in Theramore for Alliance (If you don't see Tervosh there, wait a few minutes, he should be back soon).

Barrens

Deviate Hides
Gotten in a small cave above Wailing Caverns, slightly tricky to get to.

Dustwallow Marsh

'Swamp Eye' Jarl's quests
His house is a on the right side of road a ways out of Theramore. Bring 3 soothing spices with you.

Stinky's Escape
Escort quest, north of North Point Tower.

The Orc Report
Starts from grave next to 'Swamp Eye' Jarl'.

Thousand Needles

Lonebrow's Journal
Starts at a book in the hand of a corpse near the bottom of The Lift. Leads to Razorfen Kraul.

Feralas

Doling Justice
AKA 'The Sprite Darter Quest' The elves are on a ledge west of the darter cage. When the quest dead-ends, return to the elves.

The Giant Guardian
Leads to an escort quest. Take her straight east to the road, then follow the road down then back west to the quest end.

Un'goro

Williden's Journal
Starts from a book that drops off just about any creature in Un'Goro.

It's a Secret to Everybody
AKA 'The Zelda Quest' Starts at a wrecked boat not far from Un'Goro entrance. Very long questline.

Finding the Source
Starts at a goblin on the west side of Un'Goro

Azshara

Kim'jael Indeed!
He is at the top of a large hill in northern Azshara, near a satyr camp.

Stormers and Rumblers
Questline starts from a water elemental lord on an island in SE Azshara. It eventually leads to Molten Core. There are faction requirements for some of the quests.

Silithus

Brann Bronzebeard's Lost Letter
Letter drops off any of the bugs in Silithus, including the non-elites from killing the druids. Easy 8300 exp if you aren't 60 yet.

Tanaris

Ship Schedules
Starts from item from the footlockers that drop off pirates.

Tooga's Quest
Escort quest. He wanders around SW Tanaris. He follows you, so you can mount up and lead him fairly fast across the desert. Just be sure to not get too far ahead.
Western Plaguelands
Eastern Plaguelands
Alterac Mountains
Hillsbrad Foothills
Arathi Highlands
Wetlands
Loch Modan
Dun Morogh
Badlands
Searing Gorge
Burning Steppes
Elwynn Forest
Redridge Mountains
Westfall
Duskwood
Swamp of Sorrows
Blasted Lands
Stranglethorn Vale


Western Plaguelands

Better Late Than Never
Starts in the Felstone farmhouse.

The Wildlife Suffers, Too
Starts at a dying Tauran in a house at Writhing Haunt Farm

Mrs. Dalson's Diary
Starts at a book on the floor of the Dalson barn.

Unfinished Business
She is down a gully east of the lumber mill in north WPL

Mrs. Dalson's Diary
Start by clicking on a diary on the floor of a barn

Eastern Plaguelands

The Lost Tablets of Mosharu
Its a follow up to the Hakkar egg quest in Sunken Temple, you get it from a dwarf in Steamwheedle, it leads to EPL for 2 tablets, then back to steamwheedle, then the next quest goes to LBRS (can only be done 5-man), then talk to a troll nearish the dwarf to get a nice cloak reward.

Augustus' Receipt Book
Starts in a house in Terrordale. Same house as Egan.

Tirion Fordring's quests
He is next to the river on the northern west side of EPL. Long questline, eventually leads to Stratholme and beyond. Nice rewards.

Alterac Mountains

Foreboding Plans
2 quests Start at documents on a table in the Syndicate camp north of Tarren Mill. Min level 27.

Hillsbrad Foothills

Assassin's Contract
Kill shadowy assassins in Southshore to start this quest.

Arathi Highlands

Crystal in the Mountains
Necklace drops off level 30-40 creatures all over. The necklace is wearable and you get to keep it after doing the quest, though it has no vendor value.

Pirate Cove quests
Several quests hidden back in this cove. You can see the boat when you fly north to Southshore.

Sully Balloo's Letter
AKA 'That letter under the Thandol Span'

Wetlands

James Hyal
AKA 'Dustwallow Marsh Inn for alliance'

MacKreel's Moonshine
AKA 'That quest out on the Thandol Span that's a pain in the butt to get to'

Loch Modan

Farstrider Lodge quests
4 quests. Including 2 of the few timed quests in the game. Plenty of time unless there is competition.

Dun Morogh

Hurley Blackbreath
Starts in Kharanos, and an optional pre-quest in Blasted Lands

Tundra MacGrann's Lost Stash
Climb the hill opposite of the yeti's cave to find the quest.

Grime-Encrusted Ring
Random drop off any of the dwarves.

Badlands

A Sign of Hope
Starts from a piece of paper on the ground at Hammertoe's Digsite in Badlands, long questline, leads to Uldaman.

Searing Gorge

Caught!
Starts at an outhouse in SE Searing Gorge

The Key to Freedom
Searing Gorge outhouse quest

The Horn of the Beast
AKA 'The Key to SG Quest' Kill a dino in a cave in SE corner to start quest

Suntara Stones
Escort quest starts in pit near the outhouse. Don't forget to pick up the note at end of escort.

Burning Steppes

A Taste of Flames
Can use the molt from the main Searing Gorge quest, or he will summon a drake to be killed.

Elwynn Forest

Mazen's Behest
Starts near Stockades, leads to Swamp of Sorrows.

In Search of The Temple
This questline starts in the bar in the Dwarven district of Stormwind and eventually leads to Sunken Temple.

A Meal Served Cold
Starts at the inn in the mage quarter. Has a timer, but it can be bypassed easily.

Feast At The Blue Recluse
A follow up to Stinky's Escape.

Harlan Needs a Resupply
Starts from a man that wanders around the trade district.

The Collector
Gold Pickup Schedule drops off the Riverpaws in Elwynn

Redridge Mountains

Missing in Action
An escort quest that starts deep inside the orc champion cave

Theocritus' Retrieval
A dropped item that starts a questline

Westfall

Captain Sander's Treasure Map
Starts from a map that drops from murlocs

Captain Grayson's quests
He is at the lighthouse in southwestern Westfall

Sweet Amber
Semi-long questline that ends with a trinket reward. Starts at dwarf in mountains of southern Westfall.

Furlbrows Deed
Item drops off defias in Elwynn and leads to Westfall

Cluck
Find a Westfall chicken, then /cluck at it till it talks to you. No, no, you don't look silly...

Red Silk Bandanas
There are several bandana quests, but most people miss this one that starts at the top of the westfall tower

Duskwood

The Weathered Grave
Starts at a grave between the hermit and Sven's camp, outside the graveyard.

Seasoned Wolf Kabobs
Requires Journeyman Cooking to get the quest

An Old History Book
Dropped by most undead, ogres & worgen.

Swamp of Sorrows

Magtoor's quests
He has a quest, and also a wandering creature drops an item that leads to him.

Essence of Eranikus
Starts after killing the final boss dragon in Sunken Temple. Goes several steps, then questline dead-ends.

The Lost Supplies
Repeatable quest to get Stormwind rep.

Watcher Biggs' quests
South of the road before you get to Blasted Lands.

Jammal'an the Prophet
Starts at Atal'ai Exile in Shadra'Alor in Hinterlands and goes to Sunken Temple

Blasted Lands

You are Rahk'likh, Demon
For Alliance starts at top of Nethergarde tower. For Horde starts at Swamp of Sorrows, Blasted Lands border. Very long questline.

Stranglethorn Vale

Jungle Secrets
This quest starts across the road from the northern STV graveyard. You need to be there when the alliance guard gets attacked.

Cortellos Riddle
Starts from a scroll picked up in the ships off the southern tip of STV. It can be in any of the 3 ships.

Message in a Bottle
Open bottles on beach east of Booty bay till you find quest, then swim over to the island.

The Monogrammed Sash
Kill the screaming giant on the island with the huge goblin statue on it. You will get the item to start this quest.

Nat's Measuring Tape
Starts from clicking on a battered tackle box