If it's there, it should be under Window/Preferences, but I didn't see it.
You most likely would control it from your GUI desktop control panel (Gnome or KDE), where it would be consistent with all apps on your desktop.
There's also a cool little utility that you can get that senses when you're typing near the mouse pointer and hides the pointer so that the text isn't obscured by it, but that's an add-on that I haven't been able to get running on my current system. I think it was built into my old Amiga, and I miss it. Mouse pointers are often in the way, since select-via-click followed by typing is a frequently-done thing.
An IDE is no substitute for an Intelligent Developer.
Come on, there should be a lot of people working on Eclipse in Linux who hate the blinking cursor. I accidently disabled the cursor blinking under Windows but there seems no way to do this in Linux.(Fedora5).
Eclipse is not a "Java application running under Linux". Linux itself has no GUI. The X window system is an optional graphical application rendering and control system that runs under Linux (I have servers that don't install it for resource reasons and are thus no more "GUI" than the original MS-DOS). Installed on top of X, you have your choice of Window Manager/Desktop systems such as KDE, Gnome, Enlightenment, Sawfish, OpenStep, etc. Without the GUI add-on layers, Eclipse won't even begin to run.
There are 2 different desktop flavors of Eclipse available for Unix: the Motif one and the GTK (Gnome Toolkit) one. You don't need Gnome to run GTK, and in fact, the Gnome version of the "Windows Registry" on the account is so damaged I can't use Gnome, so I'm using KDE. . I've tried the Motif version as well, but Motif is a rather antiquated GUI and it shows.
The GUI systems and Java are joined in the "write-once, run-anywhere" spirit at a few select points. AWT is where most of the contact is made between GUI apps and X (and ultimately the graphics hardware). Another contact point is PLAF - the Programmable Look And Feel part of Swing. PLAF, in particular interacts with the Desktop manager more than it does with the lower level graphics functions, deferring them to AWT. And I can assure you that PLAF is fully aware of the desktop environment, since every so often it gives me rude reminders to that effect.
In actual fact, Eclipse forgoes AWT and Swing for its own windowing toolkit (SWT), but this, too is in contact with the various components that make up a GUI desktop.
The places where UI preferences can be set on the KDE desktop are many, and so far I haven't found anything related to the cursor blink rate that Eclipse was listening to (or Firefox either), but I can't state definitely that Eclipse actually ignoring all possible setpoints, since I may not have found the one it actually does listen to.
I recommend inquiring at eclipse.org to see what the authors themselves have to say about it. And feel free to file a bug report with them if they don't come up with a good answer. While the default cursor for Eclipse doesn't bother me personally, I've worked with systems that did have annoying cursors, and so I can certainly sympathise.