I've been using Chess Nut which is US Chess and FIDE compliant. It is free for tournaments of all sizes and the most user friendly, feature rich application that I've used. I'm a US Chess Tournament Director and Club organizer. Chess Nut dot Club

Bear in mind, I have not ever been a TD but I am investigating the Sevilla program.

I can't figure out how to tell Sevilla not to rate a forfeit or bye.

Games tab->right mouse click->Edit Game brings up Game Data.

Then select Result option. What do the results with an R after them mean (e. g. 1-0R)?

Is this a standard way of notating results?

Nope.

Don't think of chess as a tennis tournament.  In a tennis tournament, the goal is to maximize the odds of 1 vs 2 in the final.  The goal of the Swiss system is to have the final round be equal on every board.  So ideally, 1vs2 3vs4...127vs128.  In order to do this, in round 1 the top player plays the top player from the bottom half of the ratings list.  For these purposes, unrated players are placed below all the rated players.  This way they play someone near the middle of the pack in the first round.   

In subsequent rounds, the goal is to have players of equal merit (score) playing each other.  If there's an odd number of players with the same score, a player from another score group is put in the mix.  (Usually, the lowest rated player in the top score group plays the highest rated player in the next score group).   

This is the best way to do things, but it does allow for relatively strong players to play "Swiss gambits".  That is, there are occasional draws or losses in early rounds due to a strong player planning for easier competition to get the desired final score.  There are few successful Swiss gambits in part because in a tight field there just aren't many "easy" pairings and in part because the mindset of someone who does this is one of someone looking for an easy way out.  And while he may place, he won't win the tournament.  Anyway, the USCF Official Rule book also has FIDE rules, but they're just about identical when it comes to Swiss pairings and tie-break rules.

I've used an older version of JBF Sevilla but this was for rather small (around 30 people) and informal tournaments, so compliance with federation rules wasn't really a concern.

I used it a few times, so it must have worked reasonably well, but I don't really remember anything else about it.  The price is right though, so you could always download it and see if it suits your needs.