Apps designed for the Mac appear in the toolbar at the bottom of the screen, but anything running under X gets lumped into the icon for X. Drag and drop doesn't work smoothly between X apps and native apps. And so on...

Still pretty much true, although things have got a bit smoother with more recent versions of the window manager. Some (e.g. OpenOffice) have "glue" applications that make things like drag'n'drop work a bit better.

This means that, generally, you'll be wanting to do things with native apps whenever possible - but most of these are not FOSS.

Well, that depends on what you want and where you look for software. I do all my development work on Mac OS X boxes and only use three applications that I paid money for ¹.

Everything else I use is either open source or freeware.

Then are the class of apps that fiddle with the GUI, so if you want (for instance) Focus Follows Mouse or Virtual Desktops, then you have to start forking out for software such as CodeTek Virtual Desktop.

Well if I wanted a virtual desktop I'll use the excellent open source Desktop Manager myself :-)

¹ For those who care I paid for:

• BBEdit - text editor
• MS Office - because it worked a lot better than OpenOffice at the time I bought it
• OmniGraffle - a diagramming tool which works a hell of a lot better than any open source product I've investigated.