[The Only Real Estel]

However, Tolkien described there to be a faint green glow about Minas Morgul, not a full blown huge beam of green light!

Creative license. I think when you stop and think about this one it's a rather minor point.

The battles seem less realistic and instead of showing the huge scale of events, seem only to diminish the appearence of size.

I missed this one, the battle looked pretty undiminished to me.

Trolls no longer look realistic and orcs don't simply look like orcs; but deformed orcs.

I actually thought the trolls were well done, for the most part. As to the deformed orc, I don't think anyone likes him, but his looks were not CGId or special effected (there's a new word for you ).

Shelob looks, instead of like a spider, like some kind of uber spider and draws the attention away from the emotional turmoil of Frodo and Sam unneccesarily

To me, Frodo sending Sam away drew more attention from their 'emotional turmoil' than anything. Either that or added unnecessarily to it.
As to Shelob I got the impression from the books that she was an uber spider.

The dead look completly silly and don;t appear to fit with the style of the rest of the film nor Tolkien's descriptions

I am on the fence with the Dead Army. However, if I had to pick out my biggest problem with them, it would probably be them wiping out the entire orc army rather than what they look like. They looked pretty realistic to me for the most part, although they did remind me a lot of Pirates of the Caribbean.

The death of Saruman was just a joke- He now shoots energy bolts from his staff, wich is a contradiction to the battle between Gandalf and Saruman in FOTR where you can see the power of the blows on the faces of the Istari and the whole thing looks a lot more like a psycological struggle. His staff doesn't merely break, but shatters and seems rather comical

The fireball that he fired at Gandalf was not one of my favorite parts of the movie--I'll agree with you there. But I don't think his death scene was a joke, other than the fact that if he really was impaled upside-down on a wheel his feet would be not be straight as he was turned under the water (I'm pretty sick at the moment, so if you don't understand that last comment, that's the reason ). When Saruman's staff is broken I almost laughed because of his reaction, rather than his staff shattering. As far as it shattering, I don't mind that much--shatter, break, it's all the same.

Obviously there is the incident with Sauron's presence becoming a gargantuan search light.

I agree with you most on this one. It looked ridiculous & went back on what Saruman was saying about the Eye in FotR, but there are whole different threads on that subject.

In summary, I think that the special effects were used well the vast majority of the time.