Star Trek (2009) was awful as far as aliens went with the CG. I felt the ships looked good enough, but many of the aliens just felt like photoshoped distortions of actors without costume or makeup.
I Am Legend is a film that I often cite as a prime example of having been ruined by CG. I love the book and was really excited about the film, but the infected are a big part of the story, and the fact that they look so goofy in their 100% CG form, completely destroys everything that was halfway good about that film. I think Matheson's book deserved far better than that. Wish some one like Del Toro had gotten a hold of it and made something really memorable, rather than it having been made to be just another disposable holiday money grabber.
And that is just it, CG is ideal for the throwaway blockbuster. Who really cares about movies like Armageddon now? These kinds of films are typically hyped beyond belief, then forgotten, ultimately to end up playing repeatedly on cheapy non-premium movie channels like TBS. Years later we stumble across these kind of films while flipping through channels, chuckle and say, "I remember when this first came out" watch it for fives minutes or less, then change the channel. It is hard to say these films are ruined by CG *cough* Transformers *cough*, because they are only made to oooh and aaaww in the first place, and not matter later on.
If you want a movie built to last, you better really think long and hard about how you use your CGI. Few guys like Peter Jackson understand this, a lesser film maker would have gone for CG orcs. The LOTR trilogy will look great for years to come. Remember the movie The Spawn? I remember that movie being visually very cool the first time I saw it during its theatrical run. Years later I happened stumple across it while channel surfing, and was pretty surprised to see how cartoony the CGI looked. The movie was made just a little over ten years ago, and its CG has looked laughable for far longer than that. It looked good in its day, but looked ancient in comparison to films that came out just a few years later. This is the same reason George redid his 1997 CG in 2004, and very likely will be giving it a third update prior to the blu-ray release (does this madness ever end? Probably not...)