MySql advises dumping the db from 5.0 and reloading the entire thing into a new 5.1 db. That's not feasible for us. We have terabytes of data. So I employ an "in-place" upgrade strategy.
STEP 0. Try out all the steps below on an old backup copy of the db to get an idea of what you are in for before attempting them on the production db.
STEP 1. SHOW CREATE TABLE for every FEDERATED table.
Are you using the new FEDERATED storage engine? None of my 5.0 FEDERATED tables would work after the in-place upgrade to 5.1. So save the output of SHOW CREATE TABLE to be able to drop and recreate them later.
STEP 2. SET GLOBAL INNODB_FAST_SHUTDOWN = 0;
The documentation for the innodb plugin says to flush all the undo and empty the insert buffer before upgrading innodb in-place. (The Percona build is based on the innodb plugin.) Turning off fast shutdown will accomplish exactly that when the db is shut down.
STEP 3. Shutdown the instance.
This step can take a lot of time. To get some idea of how long it will take, first do a SHOW INNODB STATUS. Look for the "TRANSACTIONS" section of the output; near the top you will see a "History list length" value. The larger this number is, the more undo there will be to clear. Look for the "INSERT BUFFER AND ADAPTIVE HASH INDEX" section and the "Ibuf: size" value, which is the size of the insert buffer content in units of 16K pages. The larger that is, the more deferred index updates the db will have to complete before it shuts down.
STEP 4. Replace 5.0 binaries with 5.1 binaries.
I like to build from source. So for me this involves running "make uninstall" in my 5.0 mysql source tree and then "make install" in my 5.1 source tree.
STEP 5. Replace the my.cnf file with one appropriate for 5.1 and restart instance.
Look over the 5.1 options and decide what's right for you. One variable we had to think about was innodb_autoinc_lock_mode. I perform the rest of the steps during a maintenance outage. Since in my environment all db connections are instigated remotely, I just add "skip-networking" to the my.cnf file before restarting.
STEP 5. mysql_upgrade
This script will probably try to run REPAIR TABLE on innodb tables, but it will complain every time it tries that since REPAIR TABLE is unimplemented for innodb tables. This is harmless.
STEP 6. Run CHECK TABLE FOO FOR UPGRADE on every innodb table. For every innodb table indicated as needing repairing, run ALTER TABLE FOO ENGINE = INNODB.
I wrote a python script to handle this for me. ALTER TABLE FOO ENGINE = INNODB creates a fresh copy of the table. For large tables, this can take a long time. Hopefully only a relatively small fraction of tables will need rebuilding as has been the case with my db's; otherwise you are in mysql purgatory.
STEP 7. Drop and recreate any FEDERATED tables.