Rabauke wrote a very good blog post about debugging Nepomuk and Virtuoso query performance on OpenSuse.
Also David Faure posted a Virtuoso patch on the Nepomuk mailing list which makes the Virtuoso status() command output the full queries instead of the truncated ones. I will try to get the latter into Virtuoso upstream, maybe with an additional parameter to the function.
the problem with this debugging guide is, that when virtuoso starts eating 100% cpu, the “isql-vt -H localhost -S 1111 -U dba -P dba” command will stall as well. I’ve tried it couple of times, but unfortunately, I’ve never succeeded in connecting to the db (I’ve killed the process after like 2 minutes, because I hate the fan noise)