The 1.4 patch (PS3) cleaned up a lot, but there is still an ongoing list, to which I will add my biggest issues in no particular order:
1. The White Phial is still broken beyond repair. Why?
2. Yngol Barrow never recovered its Coral Claw and its puzzle door is unopenable no matter what. This is stopping Urag's book retrieval quests and the other Yngol Barrow quests.
3. I still have many (the top 7 in the list) Misc. Quests in the journal as orphans. The 1.4 patch may clean up newly instantiated scripts but didn't clean up the old orphans.
4. Grand Staff of Charming and all three Bard's Quest named instruments are stuck in inventory
5. The game freezes up much more often post-1.4 patch, although the fps performance and autosave function are fixed.
6. Dawnbreaker was disarmed by a Draugr Overloard shout and promptly disappeared forever. grrrrrr.
7. "Blood on the Ice" never let me get to the part where we find the wizard not guilty and Callixto guilty, nor could I sell him the amulet. There is some cleanup required here.
8. Vald never talks, he just attacks. Makes it difficult to return his debt from Maven. He always ends up dead

All-in-all, 1.4 cleaned up a lot and made the game playable for high level characters again. Yay! Let's keep the fixes coming!
An updated list with more details, 3/1/12 - character is now Level 52 Imperial spell-sword (or Battle Mage if you prefer)
1. I now have the entire screen of MISC quests orphaned, specifically:
a. I cannot inform Leifnarr's family of his death - no quest arrow and no map anchor. Where do they live?
b. Skald of Dawnstar doesn't clear after bounty collection. No more bounties there for me

c.
Both Urag's CoW book retrievals (children of Sky and Shalidor's Writings) require entry to Yngol Barrow. Coral claw bug prevents this.
d. Stumbled upon dragon at Dragontooth Crater and killed him. Then got a bounty from Markarth to do so - he's not there anymore and the log entry won't clear.
I can't get anymore bounties from the steward at Markerth until it does.
e. The bandit leader at Nilheim is dead, dead, dead, but the journal entry remains
f. Both Fjola and her husband lie dead, one by my hand, one otherwise. No joy of cleared journal entry.
2. A new weirdness - the Skyforge Steel Dagger is invisible in my "Use Grindstone" menu so it cannot be improved 
3. Who the heck is Lymdrenn Tenvanni and why am I stuck with the journal?
4. The Companions' side quests are an infinite loop of Animal Exterminations, Heirloom Retrievals and Hostage Rescues. When will Vilkas and Farkas ask me to cure them?
5. No more work being offered from the Jarls of The Reach (see above) The Rift (Nilheim bug) and Eastmarch. Did all their troubles go away? 
6. Got Frost, rode Frost, had Letresh follow me to Whiterun (?) Now Frost has gone missing. Any ideas where Letresh made off with him?
Let's have a great cleanup party when the 1.5 patch is issued!!