<p>There are some fairly powerful tools like <a href="http://www.culater.net/software/SIMBL/SIMBL.php" rel="nofollow noreferrer">SIMBL</a> or <a href="http://rogueamoeba.com/airfoil/mac/index.php" rel="nofollow noreferrer">Airfoil/Instant Hijack</a> which use code injection.<br>
As far as I understand this, these tools inject their own code in other programs. This idea sounds dangerous to me as this seems to have the potential to make perfectly stable software fragile and "buggy". Also this seems to pose security risks.</p>

<p>Should these tools be avoided for stability or security reasons?</p>

I believe it does not just refer to that
kind of code injection
for hacking or cracking a system.
It is also a technique often used in java world, with tools like
AOP
or
IPojo
.
When they make sense, they complement the current code, allowing them:
to function within a given framework (OSGI Declarative Services for IPojo)
to add functionalities (logging services for AOP)
As long as the initial code can run without that code injection, the stability is less an issue.
Stability and security - in the case of those two benevolent usages of code injection - of the injected code should be evaluated in a separate test code.