Everybody usually complains about missing this feature or that feature in Netbeans, but not me. I only work in "tic toe" programs so Spring, Hibernate, blah blah... they're not my concern.
+ Loading at startup is more slow: These days Netbeans 6 needs to spend more time to load. I only installed Ruby and Maven plugins but 45 seconds for loading is not acceptable (JDK, libraries and project are already cached, my laptop is 1.66Ghz and has 1GB RAM).
+ Expanding node is very very slow: When I expand Source Packages node in Project pane, it takes 3-4 seconds to display all packages. God, I only have 6 packages and only 2 of them contain over 20 classes.
+ Expanding code templates uses inappropriate shortcut key: Netbeans 5.x uses Space by default and Netbeans 6 uses Tab. I think it is stupid 'cause if I enter "psvn" then delete "n" and enter "m", at that time press Space/Tab and expanding doesn't work. ("psvm" + expand code template shortcut key should generate main()). But Netbeans supports to change shortcut key for expanding code template and I need to change to Shift + Space.
+ Popup intellisense list is slow too: If you press Ctrl + Shift + Space inside the editor, Netbeans will show a "Please wait..." list and you need to wait a little before the intellisense list appears. While in IntelliJ IDEA, the intellisense list appears immediately. This problem also happens even you entered some characters and the intellisense list is very short (only a few elements).
+ Missing inspections: Using Netbeans, I really miss the inspections in IntelliJ IDEA. AFAIK, at this time Netbeans 6 only has inspection to generate javadoc and remove unused import.
+ Templates are stored in Netbeans folder: If I uninstall Netbeans, I will lost my templates. It should be kept in user's folder.
+ Doesn't show error description in status bar: Netbeans can parse the source code and highlight the errors but I cannot see error description until I move the mouse over the error indicator.
Update: If I enter "nout" then move the cursor back, delete "n", add "s", move the cursor to the end of "sout" and press Shift + Space (I configured to use Shift + Space to expand code template), expanding code template doesn't work too.
Generating javadoc comment should generate closed comment: When I enter "/**" and press Enter, Netbeans should generate "*/" for me.
Update: Do not force me to use quick search: When I want to generate a constructor with several fields, I press Space to select a field then Netbeans display quick seach text box so I need to press Esc to hide that text box.
Formatting for switch statement is not correct: When I enter "case 1:" then press Enter (or Ctrl + Shift + F to format code), Netbeans does auto un-indent "case 1:" so it has same indent level with "switch (n)"
Update: Should detect JDK home automatically: You can see description here: http://www.netbeans.org/issues/show_bug.cgi?id=99745. And if they bundle up the JDK, Netbeans will have same size with IntelliJ IDEA.
Note: All the problems here I met in Netbeans 6 (latest test daily build)