The "Quicklift" hood struts do an amazing job of cleaning up the prop rod area and giving it a nice look. IMO, anyway. They look like this:
I was leary of spending the money on them but I am very glad I did.
As everyone else said, rerouting/hiding wiring harnesses and electrical components will do wonders. Rerunning hoses so they tuck away/etc. helps as well. Then to step it up a bit you can fill in all the holes in the sheetmetal, paint it, flatten/smooth out the dips and valleys, etc. The biggest thing is the wiring harnesses and having the overall engine look clean and nice.
The writeup mob mentioned can be seen up here:
http://www.soniccherry.com/ but that's just to give you an idea of how to go about doing it. At the end of the day, you can stick the harnesses wherever they fit and are out of the way. They connect to each other just ONE way, so it can't be messed up and it all basically ends up the same way. The only diff. will be how exactly/where exactly you route them out of the way (inside the fenderwell, naturally).