NeoGen has created this FAQ for using optimized BOINC clients
Optimized BOINC clients FAQ
Q: What are optimized clients?
A: Optimized clients are boinc executables (.exe files) and sometimes linked libraries (.dll) that are specially compiled to take advantage of the most advanced features of each kind of CPU. these advanced features include special processor instructions like MMX, 3DNow!, SSE, SSE2, SSE3, etc...
Q: Does it make my machine crunch faster?
A: No, it does not make your machine crunch any faster. The Boinc application itself does not crunch anything, it merely manages the crunching apps, starting and stopping them at defined intervals to ballance the cpu time across all the projects that you are crunching for.
Q: So, what good is an optimized client for?
A: Boinc claims credits for a given workunit based on the time that it took to complete it, and the speed of the machine itself. The optimized Boinc client using the most advanced cpu features gives a higher speed value for the machine's benchmarks, which in consequence makes boinc claim more credit than the regular client on the exact same machine. Besides that, some optimized clients have extra functionalities not provided in the regular boinc client.
Q: So, with an optimized client I get much more credits?
A: Yes... and no. The fact is that there are very few projects where you get the credits you claim. Most of the projects calculate an average of several claims, or grant the credits of the machine making the "middle claim". (Not the highest, and not the lowest). But in general, it is always better to use an optimized client, because in case the project grants the average of claims, one or more high claims can grant higher credit for you and the people that crunched your workunit.
Q: Wait, aren't those inflated benchmark values cheating?
A: If you use a recognized optimized client then no, it isn't cheating. The benchmark values will actually show the real potential of your machine, and not the low values given by the regular client. On the other hand, if you're a hacker and you plant absurdely high values on the boinc source code and compile it, then yes it is cheating. (And yes, it has happened already)
Q: What are those extra functionalities said above, and do I need them?
A: Technically, you don't really need them, the regular boinc client already comes with everything necessary to start working. The extra functionalities can be things like reporting workunits instantly (boinc sometimes takes a while), changing the default communications port (useful if for some reason the default port is blocked or used by another application), changing the default process priority, getting more work, and many more.
Q: Where can I get these optimized clients?
A: See gamer007's List of Optimized BOINC Clients thread for a list of known good optimized clients for almost all platforms/OS'es.
Q: How do I install an optimized client?
A: An optimized client is not really "installed". What you do is install the regular boinc client as you normally would, and afterwards extract the contents of the optimized clients zip files inside the boinc folder, overwriting the files as requested. Then you start boinc as normally, and you execute the benchmarks manually once (Advanced menu->Run CPU benchmarks) just so that it records the optimized benchmark values.
Q: Is there any project that can't be run with an optimized client?
A: Any project that runs through a regular boinc client, can run with an optimized client as well. However any project that runs a custom version of Boinc (The japanese Cell Computing projects for example) cannot run with an optimized boinc client.