Welcome Aboard!
I'm new too... but I'll help with the ones I hear about most. I'm sure others here will be able to give deeper insight than me.
TMO = Trigger Maru Overhaul. This is a "super-mod" that changes a LOT of stuff (for the better) both graphically and gameplay-wise. Think of it as a free expansion pack.
RFB = Real Fleet Boat. Another super-mod. As far as I can tell, you should only use one super-mod at a time to prevent conflicts. I haven't tried RFB, so I don't know anything about it
RSRDC = Run Silent Run Deep Campaign. This changes up the missions to make them more historically accurate (no more sneaking into an enemy harbor to drop off a spy.)
JSGME = JoneSoft Generic Mod Enabler = A must-have if you're going to play with mods. This program is what you use to install mods. It's great because you don't have to go in and manually backup and replace files, this program does all that for you. And when you want to uninstall a mod, it's just as easy.
Those are the major ones I know of. Keep in mind when you're installing mods with JSGME, that the most recent one on your list will over-write any conflicting files with mods that were previously installed (unless you tell it not to, but things could get messy if you don't keep track of it... easer to plan the order of installation). So, you typically want to install your super-mod first, then any applicable patches, then campaign mods and any applicable patches, then any other little mods last (this is a guideline, not a hard-fast rule).
I run TMO, and RSRDC and install them in that order. When I use JSGME to activate the RSRDC, I get a warning telling me that TMO has already changed files, do I want to overwrite them? I say yes. Don't worry, if you go back later and de-activate the 2nd mod, the first mod is returned to where it was, so nothing is permanently changed/overwritten. I have a couple other little mods that I install afterwards.
Hope this helps.