I had been holding at a late 2.x version until my recent update to OSX-beyond-Snow-Leopard, and finally installed 3.41 yesterday. It looked horrible. I use the "table view" 99.9% of the time, and the fonts had gone from a smooth, well-sized (but not adjustable), readable, font to something thin and smaller and pixelated. I found the new font prefs, but everything I tried still gave me pixelated fonts that were a pain to read.
So, I searched their online help. FAQs, and KnowledgeBase to no avail, then wrote to their support email at 6:30 yesterday evening (Saturday. The weekend between Christmas and New Years.) asking what the fonts were in v 2.x so I could replicate that setting. I thought I’d get a response sometime Monday. Nope, around 10 PM I got my answer, and also explaining that the Java version is different and that affects the font rendering, and offering other suggestions as well. Long story short: the back-and-forth about the font rendering uncovered a bug in all platforms in the table view. About 26 hours after I wrote that first email, there's a new version of Readerware available to correct the bug.
I've downloaded and installed it, and things are back to a clean font.