Geox: Geox's patented breathe system prevents the blistering and pain that occurs when your foot sweats and begins to swell. Geox shoes are all equipped with tiny holes in the sole that allow for air flow and reduce sweating and therefore swelling. In doing so, the shoes remain more comfortable for a longer period of time. And Geox sells cute flats, heels, boots and sandals - all appropriate for work and the commute.
Aerosoles: I know Aerosoles is known for being your grandma's shoe brand of choice, but trust me, there are some very cute options as well. Aerosole shoes have extra contoured padding on the inside that make the shoes more comfortable for longer periods of time. Their shoes also come in "wide" for individuals who need some extra room to avoid blistering.
Clarks: Ya ya, I know, another grandma brand. When I was in New York City earlier in the spring I went into this store with my family and was surprised to see quite a few cute styles of flats and heels. I would not wear some of the styles, but there are certainly some options if you are really concerned about comfort and looking good. Clarks is known for being a very comfortable brand.
I wrote those in that order because that is likely the order that I would choose to go to those stores. Let me know if you know of any other brands that have a comfortable, yet stylish shoe. Geox is certainly my favourite store for comfortable, fairly inexpensive shoes for commuting to work without the pain.
Unfortunately, great shoes don't make the smelly guy on the subway go away...sorry!