For men, military style tactical boots, kept polished, can be almost indistinguishable from dress shoes, and are an order of magnitude or two more comfortable. In addition, the type with steel toes and non-slip soles are approved footwear for any place I have ever been that required safety boots.
Add a set of comfortable gel insoles to those and you will have foot nirvana all day.
For women, stick with comfortable shoes over pretty/fancy ones. Even sitting at a desk all day, your feet have a major impact on your overall comfort. Low heels or flats that match a variety of clothes can be life savers. And don't forget that you too can use the lovely gel insoles to improve comfort.
In either case, it is also nice to be able to sneak the shoes off under a desk and stretch your feet out while you work. Just keep clean feet and no one will even know. (Except the support monkey checking your Ethernet cables)
If you are sitting for longer hours than standing and moving around, wear a belt that is slide adjustable instead of one that has pre-punched holes. Remember that the longer you are sitting, the more your spine compresses and the more your girth temporarily increases (no matter how fit you are).
If you end up having to wear dress shirts and find them uncomfortably hot or cool, Under Armor and similar companies make thermal regulating undershirts in a variety of colors, including black, white, and neutral/tan that work well enough for desert and cold weather troops. They are well worth the investment in my opinion. They also allow you to slip off a dress shirt if you have to do a desk dive, dust yourself off in the appropriate restroom, and return to full dress without missing a beat.