I just ran across two helpful pages with additional information on Unicode fonts for polytonic (i.e., ancient) Greek in Windows and Linux. (Some of the info on the fonts themselves is also relevant to Mac.)
First there is a series of posts on the Nerdlets blog (Tommy Keene). The link here is to one on fonts, but there are links to several related posts further down the page that deal with configuring and using them in Windows and also Ubuntu Linux.
Second, Vern Poythress explains how to use Unicode on Linux–something for which I hunted in vain a year or so ago when I started experimenting with Ubuntu. “Keyboard Entry of Polytonic Greek and Biblical Hebrew in GNU/Linux.”
Nerdlets also has an article on how to “Run Bibleworks 7 or 8 with Wine in Linux (Ubuntu 8.04 and 8.10).” Not having a credible Bible software tool for Ubuntu was the deal breaker for me last year, so though I still have a Windows box set up to dual boot into Ubuntu, I haven’t messed with it much. Ubuntu may be the easiest of the Linux flavors to learn/use, but it’s still a long ways from the usability of Mac (or even Windows XP!). It takes more technical knowledge to do what you want to do and if you don’t already have that, it’s a steep learning curve. I’m also stuck with the older Windows box I use due to its video card not having drivers for the current version.
All in all, I finally decided last spring to upgrade my Mac instead. That’s a more expensive route than Ubuntu, but since I’m not sufficiently “techie” to grapple with Ubuntu, I decided it was worth the cost for me to get more work done more efficiently on Mac. (Now if Accordance ran on Ubuntu, I might have thought twice… 
) When it came to paying heating fuel costs, I decided to cut my own firewood and get some exercise at the same time. But for getting academic work done, I’ve decided to pay Apple to do the heavy lifting for me.
Thanks for the write-up! I’m glad this was helpful.
Switching to Linux is something of a leap of faith, to be sure, and you have to adjust the way you do things, but there are advantages as well. But OSX is a Unix-based operating system–y’all are like distant cousins–so we’re all one big happy family.
It all comes down to the software you want to run, and there are a number of great free, open-source choices for any OS. Bible software is the exception, obviously, which has no good Linux solution. Various web apps are starting to pick up the slack (like zhubert and logos online), but we’re not there quite yet…
Love your blog, by the way. It provides me with no end of great material for my Greek class!
Glad to hear from a “distant cousin”!
My guess is that the market for serious Bible software (i.e., something like Accordance) is too small for anyone to figure out how to make a living doing it in open source style. I’m still skeptical of doing it in some sort of cloud environment. Not that it isn’t technically feasible (or likely will be in due time), but I’d be surprised that those folks who own the databases necessary for this sort of work would be as interested in putting them online. It’s one thing to put up text-only works (Bible translations and out-of-copyright books), it’s something else for the tagged texts. Perhaps I’m too pessimistic, but I don’t see this happening anytime soon; if something seriously useful materializes in 5 years I’d be surprised. It’s one thing for a publisher to use, say, a Bible translation in an online environment to puff printed sales (e.g., ESV?), but it’s something else altogether when the digital databases and tools *are* the primary (and in some cases the only) value product being sold.