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When writing your own checks, there are some shell-script programming techniques you should avoid in order to make your code portable. The Bourne shell and upward-compatible shells like the Korn shell and Bash have evolved over the years, but to prevent trouble, do not take advantage of features that were added after Unix version 7, circa 1977 (see Systemology).
You should not use aliases, negated character classes, or other features
that are not found in all Bourne-compatible shells; restrict yourself
to the lowest common denominator. Even unset is not supported
by all shells!
Shell functions are considered portable nowadays, though Autoconf still does not use them (Autotest does). However, some pitfalls have to be avoided for portable use of shell functions (see Shell Functions).
Some ancient systems have quite small limits on the length of the `#!' line; for instance, 32 bytes (not including the newline) on SunOS 4. A few ancient 4.2BSD based systems (such as Dynix circa 1984) required a single space between the `#!' and the `/'. However, these ancient systems are no longer of practical concern.
The set of external programs you should run in a configure script is fairly small. See Utilities in Makefiles, for the list. This restriction allows users to start out with a fairly small set of programs and build the rest, avoiding too many interdependencies between packages.
Some of these external utilities have a portable subset of features; see Limitations of Usual Tools.
There are other sources of documentation about shells. The specification for the Posix Shell Command Language, though more generous than the restrictive shell subset described above, is fairly portable nowadays. Also please see the Shell FAQs.