Pivotal Labs certainly is one of the top contenders along with the likes of Thoughtbot and Hashrocket. If you're looking for comparable work quality to those companies but with less cost associated with less overhead, be sure to check out my profile and visit our shop's website "Found Design + Interactive":http://wearefound.com. As well, even if you'd just like to chat or toss around ideas, myself and the rest of the crew certainly don't mind helping you get started.
Pivotal Labs is well known for Ruby and Rails work, and is specifically organized for empowering startup teams while at the same time delivering products. I'm almost certainly biased, since I work there, but if you ask around I think you'll find lots of positive feedback for Pivotal's work.
We have information for potential clients on our site (pivotallabs.com). You're welcome to contact me with any questions, and I'll make sure to get you going in the right direction.
I am currently working on a few projects that require web application development and design. We are specifically looking for a shop that has experience with designing for startups that can advise as well as they can execute on a vision. Are there any companies that stand out or are known as "best in class"? Am I right in assuming companies like Thoughtbot and Citrusbyte are worth the premium they charge?