Linux: Seg-fault in the gcc toolchain. After casting about for several days, we couldn't even find someone willing to take our money to fix it. Digging into the code (ld), it's so cryptic it may as well be written in undocumented assembler. Responses from mailing lists and forums: "Go back to Windows" "Restructure your project to avoid that problem" "Why are you complaining, fix it yourself, it's open source" etc. We couldn't submit a test case, because it would have required making public a lot of code containing trade secrets.
Solaris: Seg-fault in the Solaris compiler toolchain. We called Sun, and were talking directly to dev tools engineers within minutes. They put the case on 24 hour support and had a patch for us to test a day later. We could submit a reproducible case because Sun accepted the code under NDA.
Not the kind of thing that shows up in feature bullet point comparisons, but when you have 30 developers held up on one side and the clients need the code to calculate their bid for an eleven-figure project (as in this case), it makes a difference.
In other words, Sun is at a disadvantage, since one of their main selling points requires an understanding of IT risks that most people, unfortunately, do not have. IT guys may think linux is 'cheaper' but they don't have their end-users' acute desire to minimise the already-remote chances of some random problem costing them millions in commission. Edit - it is also an unfortunate reality that being able to pin the problem on Sun (or Microsoft, etc) can save your career in a situation like this. There's no-one to blame if you are using open source and it goes wrong. The buck stops with you not just for your code, but for the code of any free tools you are using. I wish that wasn't how it worked, but there it is.
Plus, if you stay 'on piste' doing stuff that has been proven to work (you could hardly argue against Linux + apache for example), you have a relatively small chance of stepping on these engineering landmines.