CFW Comparison

rxTools 2.6

 * Easiest to set up, you only need to put two files in the root of your SD card.
 * emuNAND can be updated to the latest one, unless you're on a New 3DS, where it can't be updated past 9.5.
 * Can only use old entrypoints.
 * It includes a set of tools that are now outdated (use decrypt9 and emunand9tool instead).
 * Regionfree without any other additional software. It's not a big deal since most .cia files are already patched and you don't always need it, but it can be handy if you're on the original 3DS and you have installed a not-patched version of a game that requires more RAM (like SSB4).
 * It patches AGB_FIRM and TWL_FIRM automatically, meaning you can play DS(i) and GBA games without an additional one-time installation. This only works on the original 3DS.

rxTools 3.0 + Pasta (aka rxTools nightlies)

 * The original developer left the scene and lend rxTools over the Pasta Team, the developers behind the Pasta CFW, an outdated CFW made out of code found on Pastebin.
 * No stable release. Downloading "the latest version" should only be done for testing purposes to report bugs, as that's what nightlies are meant for and, as it's expected, sometimes it has been able to brick in the past. Pay particular attention to this if you think you might end up using anything other than rxMode. If a guide suggests you to use a particular version, that's most likely fine.
 * It includes a set of tools that are now outdated. They're supposed to have updated them, but decrypt9 and emunand9tool are still better and have more features. As mentioned above, some nightlies happened to have some bugs that could damage your system, and this has to be expected from unstable software, so pay attention to this.
 * The folder structure has been changed once in the past.
 * It works with the newest entrypoints.
 * Regionfree without any other additional software. It's not a big deal since most .cia files are already patched and you don't always need it, but it can be handy if you're on the original 3DS and you have installed a not-patched version of a game that requires more RAM (like SSB4).
 * It patches AGB_FIRM and TWL_FIRM automatically, meaning you can play DS(i) and GBA games without an additional one-time installation. This only works on the original 3DS.
 * emuNAND can be updated to the latest one, unless you're on a New 3DS, where it can't be updated past 10.2. The developers are working on this.

Cakes

 * Easier to set up (all you need to do is to put two files in a folder in your SD card).
 * Simple and clean interface. You get everything you need in a few lines of text.
 * You can enable and disable features freely.
 * It supports the newer entrypoints.
 * emuNAND can be updated to the latest one currently available.
 * It requires installation of a .cia before playing DS(i) and GBA games.
 * Regionfree requires you to install and run a .cia first. It's not a big deal since most .cia files are already patched and you don't always need it, but not having such a feature might be kind of annoying. The developer is working to add this feature.
 * mid-kid (cakes dev) bricked his own console, so development is paused until he fixes his 3DS.

ReiNand

 * Easy to set up.
 * It only works on the New 3DS, unless you use ReiNand Mod.
 * It supports the newer entrypoints.
 * It shows an image at boot that you can change to whatever you want.
 * emuNAND can be updated to the latest one currently available, even on a New 3DS.
 * Regionfree requires you to install and run a .cia first. It's not a big deal since most .cia files are already patched and you don't always need it, but not having such a feature might be kind of annoying. This feature is supposedly not going to get added.
 * It requires an one-time installation of a .cia before playing DS(i) and GBA games.
 * It supposedly includes a screenshot tool and a memory viewer, both of which can be obtained on any other CFW by using NTR.

Gateway

 * They want you to spend money on their thing. It's generally considered to not be worth it nowadays unless you already have one from when it was the only available option, but it's your choice, so if you want to support Gateway's closed source and paid software and/or you want the exclusive features this CFW has, go ahead.
 * You always need the Gateway Red Card inside your 3DS if you want to use it.
 * Trying to prevent people from using clone cards, they actually bricked the consoles. It was supposed to brick clones users' consoles, but it actually reverted back to brick "legit" GW users as well. This isn't supposed to happen anymore, as it should just bring up an error in case it finds a clone. The only clone worth mentioning now is DSTwo+, which is also an improved DSTWo flashcard for the DS. The downside of using it to launch the GW CFW is that it might not work or even lead to a brick, according to some sources.
 * It works with the newer entrypoints.
 * emuNAND can be updated to the latest one currently available, even on a New 3DS.
 * It includes an exclusive way to cheat in the games, but there are other free options for this (like NTR or the old spider exploit).
 * Games are automatically cryptofixed. Sometimes games get a new encryption, requiring you to either use a cryptofixed version of them or to update your emuNAND. Gateway will run them regardless. This is not a big deal either, as updating emuNAND is really easy and reccommende, but it might be useful in some situation or, hopefully not, in the future, in case we won't be able to update emuNAND past a certain version again.
 * It has a .3ds loader. This means you can download games and play them without having to wait for them to install. .3ds files have headers though. Be sure to use private header (meaning you have to own at least one legit, preferably not used, card game to get your own header from) as Nintendo will ban you if they see more than one people using the same header at the same time.