Very very briefly, you have 2 classes of ROMs for Android devices in general. One is based on stock ROMs for the device (TouchWiz in the case of Samsung), the other is based on Google's AOSP (Android Open Source Project).
TW (short for TouchWiz) based custom ROMs usually retain and ENHANCE the available stock apps, and give you some extra features like being able to control CPU speed, screen color values, switch DPI etc. They are also known as "cooked" ROMs, and the authors are called "chefs".
You usually get all the Samsung stuff available, unless it's a "slimmed" ROM where the chef has cut out what they feel is unnecessary.
AOSP ROMs, since they are from the freely available Google sources, can be recompiled by developers and features added, optimized or subtracted depending on the philosophy of the dev team. These are "compiled" ROMs and the developers are called developers, not chefs.
AOSP ROMS do not contain the Samsung specific features of TouchWiz like S-View or whatever "S-something" app bundled by Samsung, but since this is Android, there are either replacements or close equivalents of the same apps on the Play Store.
Note that even if you use AOSP, you DO NOT lose the S-pen function, only the S-applications that use it. Any other drawing app can still use the S-Pen.
It's all a personal preference and getting used to a specific ROM type's features. See post 9, the sifus there all use a wide variety of ROMs, and the "flashoholics" change ROMs as often as they, um, make their beds I suppose.

Choice is the key word of Android.
One thing to note, is the S-Note app. It is a fantastic piece of software from Samsung, but unfortunately it only works on the Note family. This is a form of lock in. To avoid this, I recommend HandyNote Pro or others here may recommend other S-pen note taking apps.
Ok hope that was a sufficient introduction.
alexng2208 or
antt00 or
noobi3 can provide you with more excruciating details of all the ROMs they've experienced.
oh..i seee will thanks to u n added at my S4 thread..