The use of you own brand logo during in your presentation materials is fine, but what about the use of a logo from another company or organization? It may look nice, but remember that usually such a logo is protected by copyright and therefore you may need to get permission to be able to use it in your own presentation materials.
Also you have to be careful about making any changes to the logo.
It may suit the colour scheme of your presentation if you change the colour of the logo, but usually you will find that this is not allowed.
Organizations can be very strict in how and where they allow others to use their logo.