ChemDraw

The Short Version
ChemDraw is a disgrace. No Linux version (in this day and age for the academic community!). Both Windows and Mac versions are riddled with the most ridiculous bugs. Every new release contains more junk (e.g. little cartoons of animals), whilst the basics suffer from evermore fundamental problems with everything from copy/paste, to Retina display support, to opening blank pages, to simply moving structures, to randomly closing the program ("ChemDraw has stopped working and needs to close..."). When it does run, it's heavy on system resources.

The support forums are often full of issues that go unanswered and unresolved for weeks. They are particularly fond of blaming Microsoft Windows/Office for various problems. And, on top of all this, ChemDraw is ridiculously expensive. They are plain, out-and-out raping public education institutions. They are able to do this because they have a virtual monopoly in this space. Their closest competitor is ChemDoodle, which seems like a one man operation (and he's done amazingly well, to be honest and has a Linux version).

ChemDraw software isn't smart enough to understand when it is activated by a site licence. So every year it bothers literally hundreds of people - who can do nothing about it - that it's time to get a new code.

Sadly, because ChemDraw have cornered the market early on, they have become the default. This means that if you want to stay compatible with the majority of other chemistry researchers, you're likely to need it. Otherwise, stay away and consider ChemDoodle. It's a little unintuitive and slightly less functional, but it's usable, much cheaper and offers a consistent cross-platform experience.

When John says ChemDraw is "criminally expensive," he's not kidding. The version with minimal features and lowest-tier support (Prime and Bronze) for a single, named user is $525 for a year's subscription at the time of this comment. For comparison a year's subscription to "all 20+ creative desktop and mobile apps" in Adobe's product line is $599 for a single user and comes with perks like 100GB of cloud storage and hosting for a web site.

Adobe has long been regarded as hideously expensive for a single user (and it is, but if their business model is "individuals pirate our software or use GIMP, enterprise buys it," who am I to judge?), but even if ChemDraw was flawless and an angelic choir sang in the background while you use it it wouldn't be 87% as valuable as Photoshop, Illustrator, Acrobat Pro, and Flash Pro (which are not all you get in Adobe's package).