I was reading through various SharePoint forums and found the below code snippet to upload multiples files at a time into a SharePoint Document Libarary. Posting here to share with all of you:

using (SPSite siteColl = new SPSite("http://ServerName"))
{
   //Get SPWeb object representing a particular website
   SPWeb webSite= siteColl.AllWebs["WebsiteName"];
   webSite.AllowUnsafeUpdates = true;
   webSite.Lists.IncludeRootFolder = true;
   //Get the document library in which documents will be uploaded
   SPList docLibrary = webSite.Lists["DocLibName"];
   // objFileUpload is asp.net FileUpload Object
   Stream FStream;    string fname;
   FStream = objFileUpload.PostedFile.InputStream;
   int basenamestart = objFileUpload.PostedFile.FileName.LastIndexOf(@"\");
   fname = objFileUpload.PostedFile.FileName.Substring(basenamestart + 1);
   //Upload files into SharePoint document library
   SPFile file = docLibrary.Files.Add(fname, FStream, metadata, true);
   file.Update();
}

To upload multiple files into SharePoint document library, read all the files from drive in one go and loop through the above logic to uplaod all the files into SharePoint document library.