My system configuration:

• Eclipse Neon.2 Release (4.6.2)
• KDE Frameworks 5.26.0
• Kubuntu 16.10

Enabling the Breeze GTK theme (gtk3-engines-breeze) causes tooltips in Eclipse to become very hard to read, especially when there are links in the content:

Unfortunately, changing the default link color in System Settings → Colors has no effect, regardless of whether “Apply colors to non-Qt applications” is selected or not.

The best solution I could find is to modify the Breeze configuration directly. Luckily enough, it’s CSS.

/************
 * Tooltips *
 ************/
tooltip {
  color: #eff0f1;
  padding: 4px;
  /* not working */
  border-radius: 3px;
  box-shadow: none;
  text-shadow: none; }
  tooltip.background {
    background-color: #777777; /* <-- change this value */
   background-clip: padding-box; }
  tooltip.window-frame.csd {
    background-color: transparent;
    box-shadow: none; }
  tooltip decoration { 
    background-color: transparent; }

It yields a bad-looking tooltip, but at least is readable!