I browsed through messages related to this issue? I have a few questions to the OP. How did you upgrade? Did you reindex the database? Try reindexdb and see what happens. If you used pg_upgrade, you need to reindex. I did pg_upgrade on my production db and it wasn't any faster on 9.3 than on 9.0, until I re-indexed.
Adrian: I'll try to send the query attached. My doubts are: why 9.3 is slower then 9.2 with the same database/configuration/harware/query? Even worst, why 9.3 got slower results on a better HW, where 9.2 improved on the same scenario.
Yikes, that query is above my level of expertise. Someone with more knowledge of the planner than I is going to have to go over that. As to why the change? Best guess, something changed in the planner and this query is on the wrong side of the change. So are you seeing a general slowdown or is it restricted to this particular query?