Funnel CRM lets you add your company logo. Simply click on the "Settings" from the side bar on your left and scroll down. You'll find the "Company Logo" field right below the "Company Name".
Hit "Choose File" button to upload your company logo and voila! The logo will appear in your email messages sent to your customers which includes proposals and email confirming the form has been submitted, but not standard deal thread replies.
Make sure you provide a PNG, GIF or a JPG/JPEG file that should be at least 150x150 pixels in size. The image will be scaled and cropped to fit a 75x75 pixel square.