This Addon looks for Gem slots in Items, and adds an menu where you can add Gems into that item(link) so that you can compare it to an addon which has more/less gems.
It could look like this:
If you click on one of the "empty" socket at the bottom, the menu of pre-configured gems pops up, and you can select gems for that slot by clicking on them.
If you click at one gem, it updates the itemlink so you can compare the new stats whit the item you're wearing ATM.
The menu of gem's you can put into it can be declared by user, or by item-stats (like if it's stam based it shows you tank-gems, if it has healing, you get healing gems, and also you could do it by class / spec, like prot-paladin getting prot gems, and restoration-drood getting healing gems)
RatingBuster lets you specify "default" gems; then when you view an item with empty sockets, it will pretend for the purposes of the stat summary that the sockets contain the gems you picked. For example, I've set all red sockets to +22 healing, all blue sockets to +11 healing +2 mp5, and all yellow sockets to +10 haste, so if I view an item with two red sockets and one blue socket, RatingBuster will summarize the item's actual stats, then add +22 +22 +11 healing = +55 healing, and +2 mp5, and whatever the socket bonus adds. It works very well for characters like my restoration shaman who only need gear for a single role. However, it's not very flexible, so it doesn't work spectacularly well for my feral druid, whose tanking and DPS gear generally take different gems.
Bedazzler (or Bedazzled, or something like that) does the same thing, without the rest of RatingBuster's features.
The only addon I know of that lets you play with items like you describe is WoWEquip. It's essentially an in-game CTProfiles, letting you set up different combinations of gear, enchants, gems, and even talents. You can use it to see how much you'll gain by getting all the items on your wishlist, and once you've set gems/enchants on an item in it, RatingBuster will show you the difference between that and your currently equipped item. It may be a bit more than you're looking for, but it will do what you want, sans the "automatically put healing gems in healing items" features.