No, you didn't make a mistake. The only issue you'll have for the first few months are that most of the usual PowerPC Mac applications will run in Rosetta (the technology that allows your Intel Mac to run PPC software), which means they will take a small performance hit that will only be noticeable to someone who is an extreme power user (like someone who is doing lots of filter transforms in Photoshop, for example). FOr everyday use the performance should be OK. All of the applications shipped from Apple are now available as Universal Binaries meaning that these apps will run natively on both Intel and PowerPC Macs. Within the next few months, you're going to see a lot of the commercial software makers ship Universal Binaries of their applications and most open source devs should also have their Universal Binaries available for Intel Mac users already or shortly.
If anything, look for the words "Universal Binary" or "OS X Intel" before downloading. The PPC versions should still run under Rosetta. I'm assuming that Joffice is supposed to be NeoOffice/J. This is java based and unfortunately some of the java apps are having issues at the moment. You might have to wait until they port their app to OS X Intel.