Web Development

I assume that you mean the root or C: folder.

Theoretically, so long as there are not too many files, and the files do not affect the fragmentation of the page file, they should not impact performance.

The issues with having files in the root folder of any drive is that it increases the chance of accidentally over-writing a system file, and as folders reach the maximum supported number of files, the system may slow down and crash.

I would start to be concerned if the number of files is over 100.

Another factor if the system were to be hit by a virus, the more files in the root, the more files that would be infected faster.

Chas

Having files in the root directory, won't slow down the machine unless you have FAT 16 drives. FAT32 and NTFS don't have the same problems.
Still I'd suggest moving them if at all possible, just to keep things neat (:')

if they are only files other than system files like program files, windows, autoexec.bat, you can delete them in order to speed it up.