Should I use NaCl or libsodium for my application? While looking for end-to-end encryption for my app users, I stumbled upon NaCl and libsodium. I am unsure from a security perspective which of these implementations I should use for my cross-platform app. 

Are there big differences in the level of security they offer?
(I don't have an opinion on NaCl as I've never used it. My understanding is that Libsodium uses NaCl in parts, and/ or re-implements it in others.)

As far as security goes, they should both be as equally secure. As far as I know they are both opinionated in that they don't provide you with an option to use less-secure techniques. In virtually every cryptographic primitive you seek, you will only find one or two more recent and more secure (ie. best-practice). This link elaborates on some of the design decisions:

https://libsodium.gitbook.io/doc/internals#security-first

Here is a good resource on Libsodium from Paragon - if you're using PHP you'll no doubt wind up here as the standard doco is a whole bunch of 'todo': 

https://paragonie.com/book/pecl-libsodium

You don't specify a language, however, I have used Libsodium successfully across numerous Linux kernels, in PHP, Python (pysodium), Javascript, Windows 8.1+, and Android 7+ (via Termux). I have also interchanged certain primitives from pysodium with another Python library called cryptography.io (which relies upon OpenSSL).

One thing I like is the way the library provides two interfaces in many circumstances: a 'generically named' function, and an explicitly named one. For example, you can call crypto_aead_xchacha20poly1305_ietf_encrypt which explicitly defines the cipher in use, or, you can call crypto_secretbox and allow your cryptography to be 'upgraded' in the future if a newer version emerges that modifies default behaviour.

One shortcoming I have discovered so far, at least for pysodium's use of this library, is that the api exposure for Argon2id doesn't support associated data, whereas the actual algorithm code-base in the library does:


https://github.com/jedisct1/libsodium/blob/927dfe8e2eaa86160d3ba12a7e3258fbc322909c/src/libsodium/crypto_pwhash/argon2/pwhash_argon2id.c#L136
https://github.com/jedisct1/libsodium/blob/a97ab7085fcda73f4fc7dead1a499025ceda9ecc/src/libsodium/crypto_pwhash/argon2/argon2-core.c#L470 


In practice, this wasn't an issue, as I just hashed the associated data with the password - however, this might be a problem in some implementations, especially if you're producing a PBKDF in parallel with another library's so you can exchange data (in an end-to-end protocol for example). If you're using Python, you can use the argon2-cffi implementation in most circumstances.

The lack of AES-ECB and AES-CBC ciphers has prevented me from using Libsodium exclusively on one MySQL-integration project, however, it was no drama to use cryptography.io as a bridge in that circumstance. That is how I started looking at compatibility between Libsodium and OpenSSL (via pysodium and cryptography.io).