When asked by friends & family to clean up their machine and improve start-up performance, I have a general checklist of the programs I bring along. Usually I have a pre-installed copy of Liberkey on USB, but PortableApps works too, and I use these programs to create a "repair drive" that is very portable and can easily be imaged onto a flash drive for the other user if they need to address any issues in the future. Here is my primary list in order of execution (though you do not have to run in this order - it's just my preference to catch everything):
- PC Decrapifier - A good start to catch crapware that may have never been removed from the computer after purchase.
- Revo Uninstaller - Hand pick your programs to uninstall and you can be sure all of the excess crap is removed from the registry or start menu.
- CCleaner - Mentioned in a previous answer. At this point you can clean up any other garbage left behind from uninstalls. Also has a start-up tab that will allow you to turn on/off any unnecessary start-up applications. I mean, you REALLY don't need Adobe or even Java Updater to go off automatically on boot - these are things you should run as-needed if you need that extra power just to get going.
- Soluto - An alternative to picking & choosing your start-up applications with CCleaner is using Soluto to optimize the whole process for you. It goes beyond just start-up, and addresses things that may slow down normal tasks such as browser extensions. Also, you have the ability now to remotely assist another user with the application installed via your own browser at home. It's not like VNC or remote desktop - it is just a way to quickly monitor their current performance and see if they may have unknowingly re-crapified their machine later.
- msconfig - Utilized via start menu or run command. This is probably the advanced version of items #3 & #4 above. If you don't feel comfortable tweaking your core Windows installation, then stay away from this.
- services.msc - Same precaution as msconfig - don't touch these services if you're not informed on what they do or you could really do the opposite of helping. However, Black Viper has a pretty awesome breakdown of every single tedious thing your Windows services may be doing (or not doing) so you can decide to stop or delay each one (could be 100's) in order to help general performance. He has even provided several suggested setups based on your version of Windows & whether you're going all-out barebones or prefer a more conservative Windows operation.
I think these are the basics. Obviously you could spend your life tweaking the machine, and people do that too. However, I'm just a computer hobbyist/philanthropist that likes to donate a couple hours to my friends if they're having Windows crises. Hope this helps as a start.