So this is a quick procedure to help YOU keep track of all mods and for YOU to test whether mods will conflict.
1. Create a new folder (desktop is a good place) called Mod Folders
2. Create a new folder (desktop is a good place) called Mod Classes
3. Starting with the first mod you download up until your billionth (or whatever), put the mod folder with the name into the Mod Folders folder. This folder will almost be like a backup for every mod you decide to use.
4. Copy all the classes and folders in that mod folder into the folder Mod Classes. I do not know about Windows or Linux, but on a Mac, if one of the classes were to be the same name as an already existed class, then a message will popup asking if you want to replace or stop. THIS will tell you that there is a good chance that mods will conflict. Of course, some mods integrate other mods' classes, so you will need to check on that mods forum whether they do conflict, but I am sure no developer wants to waste time answering if every mod you have will conflict or not.
5. If no mods conflict, copy the classes and folders from that mod into your minecraft.jar
6. Enjoy with (hopefully) no errors!
P.S. Delete the META-INF folder whenever you want to add mods. It seems like every mod tells you to do this.