If you are on a Windows OS use explorer
If you are on a Mac OS use Finder
If you are on a Linux OS use w/e shell your distro has.
Seriously for something like roms I find a folder titled gbaRoms is all I need. I a few sub folders. One for Pokemon, one for MegaMan, one for Mario, one for Link ect... any franchise that had a bunch of games I just put into a sub folder. The rest are just in my gbaRoms folder.
Samething with photos and music. It is my personal preference not to use file management programs, I don't see the pont. It might be your preference to use programs like iTunes and photo browsers ect... What is a shell's main purpose for? GUI to file access. The only time I'll use a file management program is to edit metadata and even then you can use terminal commands most of the time.
I use an ez-Flash iv so that gbaRoms folder is just full of zip files of all my ROM dumps. The ez client (which adds a blank save file and patches the roms) can find the roms within the zip file just fine.
File management progrmas can get funky with your roms, actually any filemanagement programs. They like to either trap your files into a database or some similar structure, and they also have problems forgetting where its put your files sometimes, due to a variety of issues. Linux has a few really good photo management programs like shotwell that will just look at a folder to find it's content and nothing more. They're just a fancy shell to make things easier, I still prefer my OS's shell over it.
For roms your best bet is just folders. Make sure you have mutiple back ups. Copy on your main computer, copy on an alternative computer, copy stored out side the house, copy stored on an external HDD in the house. With roms you could even get away with using drop box.
I have a zip file of my entire ez-flash iv microSD card's contents stored in my drop box (I also don't see why ppl complain about GBA flash cards not being SDHC, I have a GB microSD card and it's 25% full and I tried to fill it, collected ROMS of games I might possibly play in the future. But the truth is, you can't play more then 3 - 4 games with in one charge cycle. So 2gbs on a SD card is excessive) If anything happens I just format a new SD card, and extract into the root of that.
Drop box is great. It works like a magic pocket that is the same on all your trousers (that is how they explain in). You have this folder in your /home that is syncs to their server and then they make sure that folder is the same across all your computers you installed the dropbox program on. So if I make changes to my gbaRoms folder on my iMac, and then get on my linux computer that file is in the same folder, and also on my PC.
If you want to sign up: http://db.tt/3hehv8a
I would say just a folder in a dropBox account, you can also access dropbox from their website. So if your house is bulldozed by some freak accident or an ex-GF or w/e burns it down, you can go to your public library or get a new computer and get your stuff.
It is cloud storage, while an encrypted connection, so your data is going to their server so that in itself is a security hole but it's relatively. Unless Anon, AntiSec or LulzSec picks a bone w/ them. Just don't put your US SSN# in a txt document in there or anything you don't want stollen. Roms are perfectly fine to store then as well as photos. Anything you can't find on piratebay is smart to back up. My music I can reDL in the event of a disaster. My roms and photos, I'm not re buying all those cards (if they get destroyed somehow) and reDumping them all, and I can't time travel yet to retake all my photos so I back that stuff up.
again sign up link: http://db.tt/3hehv8a
Go sign up and go organise.