As noted in several places, some applications feel somewhat sluggish in Ubuntu Jaunty compared with Intrepid if your system has an Intel graphics card.
There isn't a great solution for X in general yet - some options involving X.org tweaks and replacement X packages are discussed here
Applications which render a lot of text seem to be affected quite a bit. For Qt applications there is a simple workaround, in Konsole the workaround makes tab-switching much more snappy. Start Konsole with the raster graphics mode:
konsole -graphicssystem raster
This also works wonders on the Mendeley Desktop research management software which I work on.