Yeah, I've been "through the desert of #ifdefs on a thread with no name" too. Tens of thousands of lines of code with more preprocessor stuff than actual C code because it had to work on five different proprietary MS-DOS based compilers for embedded processors. My job was enabling this twisted mess (which was also its own operating system) to be built as a Linux application without breaking anything in the other builds... 

The current client code is certainly better than that by far. That still doesn't make it an ideal base for building more complex bitcoin enabled applications on it. And even if bitcoind itself isn't all that bad, the GUI is really in need of some serious professional attention by people who know a bunch about design and usability issues, not just about algorithms. Unfortunately most self confessed geeks, including myself, are far better at the latter...