You can get rid of all of the dirt, mud, grime that's built up in your engine bay; and that will make it a whole lot cleaner.
If you're talking about all of the "useless junk" that Toyota put under your hood, there's nothing that you can remove that won't have a negative effect on something. Toyota didn't put stuff under the hood just because they had boxes of stuff laying around that they had to get rid of, you know. If it's there, then it's there for a reason.
You can always move stuff under the fenders, or make it so it's less noticeable; but never remove something without knowing exactly what it does, and why it was there.