I've actually run business Linux desktops for years, and I had endless problems.
* Random GNOME profile corruption. Lots of it. XFCE was no better, just different corruption issues;
* OpenOffice bugs and crashes;
* OpenOffice crashing, starting "recovery" but failing to find the tempfile it's trying to recover, and endlessly trying to recover that file every time the user launches it from then on;
* Mail clients (Evolution or Thunderbird) crashing but leaving dead processes around that had to be manually killed before they'd relaunch;
* Painfully difficult and buggy central configuration and management of things like desktop profiles, mail setup, etc;
* Handling of archives in email attachments, those horrible broken outlook TNEF files, etc, sucked;
* Printing was painful and buggy despite my being quite careful to get only native PostScript printers. Various apps would generate broken PS in all sorts of exciting ways, or CUPS would set job options that printers would choke on, basic printer features were unusable, etc etc;
* Random app devs who decided to call umask(0700) and override the system umask before creating files, because OBVIOUSLY they know better than the user and sysadmin what the file/dir creation perms should be;
* Numerous apps that'd suppress the setgid bit when creating new subdirectories in shared working trees, leading to more permissions issues;
* I was nervous about even minor upgrades to fix bugs, because for every bug fixed there'd usually be three new exiting bugs;
* For the Windows desktops (for a few users who needed accounting packages etc) using Samba for roaming profiles, *tons* of profile corruption issues, endless printing problems, incredibly poor performance, and difficulties interoperating with the Linux desktops
These were "basic users" who needed little more than word processing and occasional use of other simple document exchange, PDF viewing, printing (oh god, so much printing), email and simple attachment handling, and image viewing/sorting/saving. They weren't doing anything complicated.
Windows 7, Active Directory, and Group Policy were an incredible breath of fresh air when we bit the bullet and switched over after acquiring a Win2k8 R2 server for unrelated reasons. Sure, they have plenty of problems - but wow, did it work better overall. Things like volume shadow copy snapshots of server-side roaming profiles were a huge improvement over periodic bacula snapshots of bits of user homedir state.
The main problems we had with Windows were with roaming profiles - and were caused by obvious bugs in OpenOffice, Firefox (moved to Chrome which was better), etc, especially keeping piles of temp state in %APPDATA% not %LOCALAPPDATA% where it should be, modifying SQLite databases directly on remote storage, etc. These apps don't get tested on "business network" type setups, with roaming profiles and redirection, and they don't follow MS's recommendations on file layout etc. It shows.
The only serious issue I had with the Windows deployment was that %APPDATA% redirection for roaming profiles is horribly broken with caching enabled; the sync tool just throws a spak, gives up, and waits for the user to resolve conflicts. It's quite capable of creating conflicts even if there's never any connectivity problem, and the results are messy. Once I disabled offline access and caching for %APPDATA% (a significant performance hit, and it meant that if the server was down even briefly all clients would just freeze) the sync issues went away, but it wasn't a great compromise.
I wasted a huge amount of time babysitting the Linux desktops. I reported so many bugs, wrote so many patches - even though back then my C programming was
I use Linux on my laptop for work, and I'd hate to use anything else. Though with the KDE4/GNOME3 thing I'm getting less fond of it. For basic end users, though? Nope. No way, never again.