Adding to ICXRa's post, BOINC also have multi-cpu-support and multi-project-support with configurable resource-shares between them.
Variable credit for different wu, meaning "turbo-wu" only using 1 minute to crunch gives very little credit while VLAR gives more credit than normal wu and so on. Some projects also have multiple applications/wu-types, and the crediting is comparable across them and across projects.
BOINC keeps track of who got assigned a "result", and only this user can return this result, and can only return it once.
Credit is only given after result validated, in seti a wu isn't tried validated before got 3 "success"-results.
This means it can take some days before getting the credit, but you're also sure anyone intentionally or unintentionally (like too much overclock) only returns garbage will not get any credit for this garbage.
SETI@home for BOINC have inserted the validated results into the science-database for over a year, so even during half a year of beta-testing the BOINC-version did meaningful science.
The "core client" of BOINC must be manually downloaded and installed, but the science-applications is automatically upgraded. This means, bug-fixes, improvements and new applications is easily upgraded.
Also means can fairly easily start using data from other places than Arecibo.
In seti "classic", every wu have now on average been crunched 8.03 times. :Q and still increasing so probably more like 15.
Under seti for BOINC, every wu is only sent to 4 different users, and tried validated with 3 results, only if errors is the wu sent more times.
This means, the BOINC-version is more than 100% more effective doing science.