For the web site, we choose a clean, original, blue, professional feel to the site. We created a custom logo which was later incorporated into the software. The web site is a pretty simple ASP.NET site with the code in C#.
For SEO purposes, we followed the basics: put concise and descriptive text on the pages and get valid, legitimate links coming into the site. WebMarkers went to a PageRank 4 pretty quickly, and it's maintained that same PageRank since then.
For the portal, we developed it in ASP.NET using C# (again). The project had a shared codebase which we wanted to take advantage of. It's a good portal, and we are currently redeveloping it to take advantage of some Ajax functionality.
The web service was also written in C# and supports multi-part file upload/download streaming with resuming capabilities and with progress notifications. This web service is using DIME attachments, but a slightly modified implementation of DIME to fit our needs.