Can I find links in the system that point to certain files throughout the system?
 

RPM's might be easier but source is usually better (in my eyes). One problem I have is I like to install all files to a specific directory. When I try to upgrade something I have I have to try and find out which links throughout the system I have to change so that the system looks for my version as opposed to the old version. Is there a convenient command that will echo back all files in the system that link to a specific file?

Your question is not properly phrased.. on a similar note, rpm's can be updated and you dont have to keep a track of where everything is installed.
locate is one of the commands. You are better off using rpm system, there is a reason its called Packet Management System.

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The reason I said I prefer source is not everything comes in rpm format, rpm packages aren't released as quick as source, and I have less dependency issues with source. For example I just downloaded MPlayer. The RPM package wouldn't install because it said a file wasn't found but the source worked beautifully (it was the same version). I've had issues with quite a few RPM packages where the source worked fine and was usually newer but the RPM didn't work.
Also I'm planning on going with Gentoo and FreeBSD and they are both source based, with package management systems. In my eyes, if you work with source it gives you the ability to work with any *nix system. I also use the command prompt for everything for the same reason.

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I checked the locate command and I didn't see any options to find where links point to. Locate seems much weaker than the find command. I realize the value in it is speed but you'd think they'd throw some better filtering options.