Here's a couple of my favorite gems, a few of which I only found on my most recent re-install a month ago.
http://tesnexus.com/downloads/file.php?id=6472 - I found this one day while simply browsing the hundreds and hundreds of pages of mods on Nexus. It adds several different kinds of torches to the game including Dwemer flares, upper-class torches, and welkynd-powered torches that last forever. The "Deluxe Torch" is my favorite.
http://planetelderscrolls.gamespy.com/View.php?view=oblivionmods.detail&id=435 - Changes well behavior to give you a static magicka boost instead of the vanilla buff. (Recently I've been using http://tesnexus.com/downloads/file.php?id=9544 for its well functionality, however.)
http://www.tesnexus.com/downloads/file.php?id=5392 - This very simple mod just adds a lot of depth and character to the miscellaneous scraps of paper littered throughout the game world. I find it 100% necessary, especially when used in conjunction with Oblivion XP in which you gain experience for reading things.
http://planetelderscrolls.gamespy.com/View.php?view=OblivionMods.Detail&id=2835 - This mod adds three documents to the world: one for The Collector quest, one for the Shadowbanish Wine quest, and one for the Daedric princes quests (
The Book of Daedra). When read they mark your map with the locations of the relevant dungeons / shrines for each quest, hence eliminating the wild goose chase. You can't fast-travel to the locations, you just get the location on your map. Each document is lore-friendly and still needs to be located within the game, they're not just given to you.
http://www.tesnexus.com/downloads/file.php?id=5478 - This is a great mod in its own right, but it's fantastic for immersionists whose characters tend to fight tooth-and-nail for every pound of encumbrance. Simply allows you to walk up to an alchemical tool and activate it like you would anything else in the game without having it in your inventory.
http://www.tesnexus.com/downloads/file.php?id=17150 - I use the COBL version of this mod. It adds a small single-mast sailboat to the game that you can purchase, live on, and sail either manually or automatically (to Anvil, Bruma, Leyawiin, or the IC). Manual sailing can get a bit glitchy when you maneuver too close to land, but it's usually easy to rectify when you run aground. This mod is a must for anyone who wants to base their operations at sea, or just wants a more interesting way to fast-travel between the ports.
http://www.tesnexus.com/downloads/file.php?id=11495 - This is my favorite of the Alternate Start mods. You arrive in Cyrodiil by ship, similar to the opening scene in Morrowind, and fill out a series of Immigration Papers as character creation. You're also given some extra options including your profession, social status, wealth, and whether or not you bear any diseases. After leaving your ship at Leyawiin, Anvil, or the IC you're told of a dream you had involving the Emperor's murder and that you distinctly saw the Amulet of Kings taken away from the scene in the jaws of a rat...
http://www.tesnexus.com/downloads/file.php?id=5243 - It always bothered me that I couldn't sit on steps or fallen logs and that sort of stuff. Problem rectified.
There are also plenty of little tweaks available to the Wrye Bash user. Personally I adjust the arrow recovery chance on creatures to about 70% and increase the speed of magic projectiles to x1.6. I'm sure there's a lot of other great tweaks and mods out there that I still haven't seen, but these tend to always show up in my load order.