I am currently designing the website for a new startup. I have 2 options (so far) for the size of the logo.
I was wondering if having the smaller logo would affect my branding at all. It would be in the "normal" logo spot, but like I said, it would only be about 30 pixels tall.
I believe having a "visible" regular sized logo, such as the one in this page with the text "OnStartups.com" would help your brand more than the smaller logo.
The small logo displaying "StackExchange" in the top left corner of this page works well with web-based applications where your brand is not as important as the amount of real space dedicated to the web-based application. Just a thought.
The logo is only a part of your online branding. It should fit well in the overall color palette and design of your website. An experienced designer can help you to make sure that your entire online presentation contributes to the branding of your business.
If designing the logo, make sure its done in vector format. Also i like to have a full color version and a black and white. The reason for this is that you can use the logo on other company collateral such as signs, shirts, and stationary.
Give them the logo in many sizes so that they can put it in their media-kit or share it with their pr firm. Sites that write reviews on their site or product will apppreciate the high resolution logo .