When selecting a project during issue creation, the user is presented with a drop down of projects to choose from. In most instances this list is small and it is easy for the user to choose.

However, in my company's case we are dealing with potentially hundreds of projects and need an easier way to filter the list and find what they are looking for.

I propose that you make the list configurable. Typically each user only cares about <5 projects at a time, so let them choose which projects are listed in the drop down through some other means (a link next to it called configure project list where a user can then pick once from the large global list which projects they care about). This way the list is always managable no matter how many projects you have or save for the future.