OK, I definitely have some thoughts on this. I'll compare and contrast (in 500 words or fewer!) the two full-time jobs I've had. They're both Internet companies, but they're polar opposites in terms of size, attitude and, conveniently enough, space:
Public Interactive/Newmarket Network:
When the company was called Newmarket Network and varied around 7-8 people, we were all housed in a large warehouse-type space in Boston's Leather District. The Leather District is a few blocks downtown consisting largely of 3-4 story brick lofts which, at the turn of the century, were the site of leather manufacturing plants. Today it's a mixture of Internet companies, very expensive renovated lofts, and upscale commercial space.
Our space was one room, with a kitchen alcove and two bathrooms. No private offices or conference rooms. The floor was concrete, so echoing was a real problem, and there was very little privacy: if we wanted to, we could easily hear the CEO talking quietly on the phone. We built a small number of websites with an even smaller team, and as a result spent most of our time working closely together. The open environment faciliated this; if I needed to ask H---- a question, I could just start talking at my desk and she'd answer. It also forced the CEO to be much more up-front about which investors/clients or prospective employees he was talking to -- we could see them, after all, and usually hear what was going on.
The space had large windows on three sides, which meant there was almost no need for overhead lights (a plus), but also that some people suffered from terrible glare problems. They'd break apart cardboard boxes and tape them to the windows to cut down the sunlight.
Because the company was under (or not) funded, the furniture was mostly "found". The desks were actually plastic sawhorses with unfinished wood doors on top -- very lousy ergonomics and I in particular suffered, I think, some permanent hand damage from having to type too high (I always need to use a keyboard tray now). The chairs were largely scavenged from other offices which had closed and thrown out their equipment.
Eventually, Newmarket Network grew and changed its name, and we moved to a larger space still in the Leather District. It had multiple offices (most large enough to hold 2-3 people) and some open communal areas. There were also private conference rooms. We got real furniture and painted the walls funky colors.
Activity in the office began to center around those offices where people needed to be. As the tech lead (and the default replacement for my manager, who went on maternity leave), my shared office space tended to be an activity center. Smaller rooms + lots of people meant a lot of noise in there, and it was difficult for people who shared to be comfortable. However, all the teams (graphic designers, techs, project managers) were still grouped close to one another and I think worked well together.
When they expanded again, we acquired the floor below, and the decision was made (against my will) to move the programmers downstairs, away from the graphic designers. Web companies _depend_ on the interaction between these two groups, because in no case can a web site be designed and implemented in a vaccuum. There was a real communication breakdown after the move, especially for new employees who then found it difficult to meet people outside of their own group. The cohesiveness of the company really fell apart at that point.
Digitas:
For that and a variety of other reasons, I left and went to Digitas, which is a large web consulting company. Digitas produces web sites and web content for Fortune 500 companies -- AT&T, American Express, FedEx. Boston is the home office and there are 1600 people here, plus smaller offices in New York, SF, London and other cities.
Digitas Boston lives on roughly 8 floors scattered throughout the Prudential Tower, the second-tallest building in the city. When I arrived, groups were staggered throughout the floors: graphic design and tech mixed on 3 and 5, accounting on 3 and 22, HR on 19, etc. Shortly after I arrived, they decided to consolidate the groups and move graphic design out of the tech areas. I heard much of the same complaints about this as I'd voiced at PI -- a web company is simply more interdependent among divisions than most other technology companies and splitting up groups is counter-productive.
The design of the office itself is thus: single-person or quad-area cubes along the exterior walls (with windows), single-person offices concentric inside that space, with winding hallways connecting them. On the exclusively tech floor (5), the overhead flights are always off. All floors have two kitchens but 5 has "the Cyber Cafe", which is a small eating space modelled after a 50's era diner, with booths and metal stools and a ceiling-mounted television. Oh, and a foosball table. Programmers are very fond of the Cyber Cafe and routinely gather there for lunch or afterwork foosball. 5 is also unique in having a large circular room off the cafe in which new hires or contracting employees sit side-by-side and work.
The private cubes are nice as cubicles go: about five feet wide, bounded on one side by a high shelf (5') and the other by a lower divider (3'). There's adequate privacy and plenty of storage space built into the cube walls. Digitas has no visible policy about how people decorate their space: there are posters, fishtanks, tapestries hung from the ceiling and stuffed animals everywhere (almost 100% confined to graphic designers or techs). There is a strong committment to ergonomics: programmers all get expensive Hermann Miller Aeron chairs and all employees get glare screens and keyboard trays on request.
What Digitas lacks is adequate communal space (conference rooms must be reserved in advance and are almost always full). After the move, it is very difficult for the individual groups to communicate smoothly. All the private offices make navigation labrythine, and even long-time employees find themselves confused about which direction they're going. Each department has a culture of its own and except for the Cyber Cafe, the tech culture is not adequately reflected.
Um, I think that's all off the top of my head, but I'd be happy to answer specific questions. Good luck!