I do skirmish in 28mm using Osprey 'Rebels and Patriots' rules. These rules for are good for large skirmishes or battles and multiple players.
'Brother against Brother' is another large skirmish set I use, but out of print and hard to find. A second edition is in the works but it is taking a long time to come out.
Muskets and Tomahawks is another skirmish set, but the ACW rules are not out yet. Rules have a little more detail and is best with less units and players on the table. I use these for AWI and FIW.
Finally there is Sharp Practice. Played it a few times. Not my favorite as it is best for smaller skirmishes with two or four players. Nothing wrong with that, but not what I am looking for.
Everyone has favorites. It all depends on how big a skirmish you want, how many players a game, and how much detail you want. Unless you specify what you want you will get tons of 'best rules' claims until the cows come home. These are the four I have played.
Regarding basing, I put my figures individually on metal washers. I recommend the same because you can always make magnetic movement trays if you want to group figures.