After much searching and testing various Linux GUI certificate authority applications I finally found one that works consistently and gives me all of the options that I need. I am not exactly sure how I missed it as it has been out for some time but XCA has turned out to be exactly what I was looking for. The biggest issue I had was creating certificates for Windows Servers in order to setup LDAPS. I had used TinyCA2, GnoMint, and various others. Both were either limited in their capabilities or failed to work consistently. I even tried to go setup full PKI systems like EJBCA and Windows Certificate Services but found them to be to difficult to pick up in the limited amount of time I had to learn how to use it.
XCA uses a Qt based GUI interface that is well organized and full featured. I found the ability to create templates a great time saver when you have to crank out lots of certificates. Plus the ability to export to any format is also very handy as sometimes I never know what I need and I can never remember the correct openssl commands to convert to different formats.