The Motorola android phones besides the original Droid use a locked bootloader. This prevents people from writing their own kernels for these phones. A kernel is the basic part of the android operating system that talks to all the hardware and handles giving apps access to your phones parts. Anyways somebody found a way to hijack a program called init, which is the first app that runs on the phone and gets everything else going. They use this hijacked program to load their own little bits of kernel, overwriting Motorola's own kernel. These roms are known collectively as the 2nd-init roms. This 2nd-init process gives rom builders the opportunity to offer features that would ordinarily need a custom written kernel. Unfortunately due to reasons nobody has quite nailed down, these 2nd-init roms tend to have much worse battery life than the roms based on the normal Motorola kernel and motoblur parts. The roms for these phones therefore fall into two types: the blur based and 2nd-init.
2nd-init roms:
Anything involving Ice Cream Sandwich, CyanogenMod, Vortex, Miui, Liquid, AOKP,
blur roms:
liberty 3, apex, Shuji
Sorry if I missed some or got them in the wrong catagories. A good indicator of what is what is how much customization a rom has. Lots of settings and features means is a 2nd-init rom. Anything recently updated is a 2nd-init rom. Personally I like the features of 2nd-init but I love the battery life and the stability of blur based roms. Everything the phone originally had when it was stock works on blur roms. Can't really say that for any 2nd-init rom.