I guess you are talking about project execution???

You can customize build.xml. These options are not customizable in UI.

Typical user doesn't know how to customize build.xml script. 

This and other possible customizations (system properties, etc.) were
intentionally omitted from the GUI. They are fairly easy to control in
build.xml and there will be instructions on how to do so for various
cases. We may include more such things in the GUI over time but I
think these are not planned for D.

I will add some property through which this could be easily
customized. At the moment the user would have to override whole target.

Note that customization of VM parameters and customization of system
properties are two different things.

Re. system properties, I have commented-out code in j2seproject's
build-impl.xsl showing how you could have them be autodefined given
the existence of project properties matching a certain pattern. Later
we could provide a GUI to set these if there is time.

Re. VM properties, I don't know of a clean way to make these
parametrizable in Ant, except by overriding the macrodef.

I was thinking about using jvmargs attribute of <java>, but now I see
that it was deprecated; I thought about: always present
jvmargs="${jvm.extra.args}" where jvm.extra.args would be empty by
default.

OK, for now user has to override run target. Something like:

<target name="run" depends="...">
 <j2seproject:java xmlns:j2seproject="...">
  <customize>
   <arg line="${application.args}"/>
   <jvmarg value="-X1..."/>
   <jvmarg value="-X2..."/>
  </customize>
 </j2seproject:java>
</target>

The problem with jvmargs is that it does not handle spaces or such
metacharacters cleanly. May not be critical, I don't know.

There is now a property you can set, at least. No GUI for D. Should
consider for E.

IMHO, but it is for very advanced users. The settings of properties is
used in many java tutorials.  Write a few lines to ant script is easy
  for users who know how to work with antscript very well. For normal
users the build script of netbeans project is too dificult. We can do
UI study for this issue.  

Current state is that newly created J2SE project has following
placeholder in project.properties:

#space separated list of JVM args for VM in which the proj will run
run.jvmargs=

So you do not have to override Ant targets now, just modify this property.

Second thing I implemented is that any property prefixed by
"run-sys-prop." is made available as system property to executed process.

Needs to be at least in user's documentation.

Would it be a big deal to expose run.jvmargs in the UI as a
single-line text field in the project properties customizer? I know
we're past the feature freeze, but it might be easy to do and make
lives of users easier. Just curious.

Of course it would be easy to do; we only haven't because of feature
freeze, and lack of a proposed UI spec for it.

Note that you can also set system properties in
project/private.properties, using a different syntax (one Ant property
per system property). This is also not available in the GUI. The UI
for that would be somewhat more complicated since it would be some
kind of table of name/value pairs.

Of course you can use

  -Dname1=val1 -Dname2=val2

etc. in your VM args to set system properties, but this is less
desirable, in particular because you cannot include spaces in any of
the values (would be interpreted as multiple arguments).

*** Issue 45431 has been marked as a duplicate of this issue. ***

*** Issue 47504 has been marked as a duplicate of this issue. ***

Assertions:

I'd like to be able to turn execution of assertions on and off via 
the project UI. Setting 'run.jvmargs=-ea' in the project.properties 
file is far from obvious for the typical user.

Two fields added to Running Project panel:
 * working directory
 * VM Options

Fixed in:
Checking in
src/org/netbeans/modules/java/j2seproject/resources/build-impl.xsl;
new revision: 1.34; previous revision: 1.33
Checking in
src/org/netbeans/modules/java/j2seproject/ui/customizer/Bundle.properties;
new revision: 1.32; previous revision: 1.31
Checking in
src/org/netbeans/modules/java/j2seproject/ui/customizer/CustomizerRun.form;
new revision: 1.8; previous revision: 1.7
Checking in
src/org/netbeans/modules/java/j2seproject/ui/customizer/CustomizerRun.java;
new revision: 1.13; previous revision: 1.12
Checking in
src/org/netbeans/modules/java/j2seproject/ui/customizer/J2SEProjectProperties.java;
new revision: 1.23; previous revision: 1.22

Re. special GUI for assertions: sorry, not covered by this, not
planned for 4.0. You can just type "-ea" (or any of its many variants)
into the VM arguments field.

Verified in dev-200408262030

*** Issue 48504 has been marked as a duplicate of this issue. ***

The GUI for jvmargs is not available on Web Projects in NetBeans 6! Is there another way to specify "-ea" for them?

asserts are *very* important for development. Why on earth does NetBeans disable them by default?

Web Application is executed within an application server environment and so the options like -ea would have to be set
for your app server VM. I'm not sure how useful that would be; only applicable for a locally running app server I guess.
You can alter your app server startup params by hand. And possibly you could file issue for serverplugins component to
provide a UI for that in server customizer.

nathanaeljones, you may want to add yourself to issue's CC list to be automatically notified about changes. You can read
my comment to your request in issue's description.

I've tried setting the server vm options, but it doesn't seem to affect unit tests...

Where could I change the unit tests jvm args on a web project? On a class project they're changed in Project Properties>Run?

Thanks for your help!

OK, you did not mention unit testing before. Well, unfortunately it is not supported. I filed separate issue for that
instead of reopening this one - issue 141464.