There are currently a few alternatives to using Cryptoloop. Loop-AES (http://loop-aes.sourceforge.net) is probably the most well-known. It provides very similar functionality to Cryptoloop, but requires kernel patches. Aes-loop is currently more mature than Cryptoloop and some argue it is also faster because it uses a highly optimized assembler implementation for AES. While this may be true, Cryptoloop is very fast. I have not noticed any significant speed differences between a Cryptoloop-encrypted partition and a non-encrypted partition. I do not know of any statistics about these performance differences. Unless I/O performance is extremely important to you, Cryptoloop should do just fine. Loop-AES offers some additional features that are not yet present in the kernel implementation of Cryptoloop. If you want to encrypt the root and swap partitions, you may want to stick with Loop-AES for now.
The Cryptoloop functionality in the standard kernel provides a stable and clean implementation without the need for extra patches. Since it is still fairly new, it may not have gotten the necessary amount of review in terms of security. You have to decide for yourself what is suitable for you.
There are other tools which allow you to create an encrypted file system. BestCrypt is a commercial product from Jetico. It allows you to create encrypted containers and has a large choice of ciphers. It also offers some nifty features such as hidden containers. It is available for Windows and Linux, which makes it suitable for interchanging encrypted containers between Windows and Linux. BestCrypt now compiles on 2.6 kernels as well. Cryptoloop can also create containers that can be moved around, by creating the encrypted file system within a file as described below. I don't know of a way to access the Cryptoloop-encrypted files from other operating systems such as Windows. In this case, BestCrypt may be your only choice.
There are other commercial disk encryption tools such as PGP disk, but to my knowledge there is no Linux support for them.