My goal with the incoming mail box is to try and always have it empty. Make use of filters to spread the emails to appropriate folders. That's the whole idea behind being able to define folders and filters to push stuff.

Also consider the  Default Mail Folder and the option to push read mail that falls through all of inbox the filters to that folder. That will save already filtered but not moved emails from passing though the filters again and again.

Make sure "AutoFiltering" is turned off for that catch-all folder too.

When I go to the New Mail folder the message "Applying Filtering Rules" appears and takes a very long time before I can use the app.

Each message in the new mail folder gets processed through the new mail filter rule set each time the new mail folder is opened.  If you have many hundreds of messages in the new mail folder try moving all but 30 into a different folder and see if there is an improvement.

Thanks. It works faster now. Though I'm surprised that the filter doesn't work more efficiently. 100 or so messages really doesn't seem like very many.

You are working on hundreds of messages at a time? Respect! My advice: use the inbox/new mail folder only for incoming, sorting and filtering of mails.

In times when mails used to be some x KB (with X element of [1..9]), fast filtering even with spamcontrol was no problem. SPAM Incresed and methods to get rid of them ... we got spamhalter. Even no problem ... if there are still only small mails. But what's normal today? If I have a look at my mailfolders, especially at my archivefolders, the amount of archived mails hasn't increased reasonable ... but the size of that folders increased exponential. Meanwhile every second mail is a HTML-Mail and every tenth mail has attachments greater than 1 MB. Happy filtering ... :-(

And even Thunderbird  and Outlook take same time for filtering. The difference: both do it in a background process and you may continue working with little impact while Pegasus can't be used while filtering.

Respect :-) 

Filters can also be optimized. Make sure the conditions that are met the most frequently are on top and use exit points when met. If you don't even if a condition is met, all the others will still be tested.