I can't say I've ever experienced the cursor freezing over the window of an opening app. The mouse cursor is usually the most responsive UI thread, even as everything around it starts to hang.

With regards to the Trackpad, in response to Tom, I'm seeing the behavior on both the external Magic Trackpad and the one built into the MBP, so it's not battery related.

They changed a lot in Lion, despite the OS's outward and feature experience being on the (mostly) light side. The trackpad system was apparently completely overhauled as part of the introduction of the newer multi-touch gestures. Hopefully it's something at least a few other people inside Apple notice too and they catch the issue.

Apart from random issues waking from sleep or Safari taking down the desktop (mostly in Snow), one problem area since the beginning of time has always been disappearing network shares. When a network share goes down, some of the OS can take forever to realize it and will seem to just hang for ages, causing other software to go with it (like Path Finder).

Processes which I've noticed can really slow things down are mdworker and mds, which are part of the indexing system used in Spotlight - and of course Time Machine backups can put a drain on disk access every now and then.