It can be hard to maintain 5 synergistic groups in a 25 man raid environment. Even then, it can be difficult to ascertain the right type of synergy needed for which encounters.
In a typical progression raiding guild you will have quite a decent number of people to choose from from raid to raid. Everyone needs raid time and everyone is not there from day to day due to real life and burn out concerns. So raid makeups need to be flexible. All that being said... Decide the type of synergy needed and what you can do to benefit the most people in the raid at once.
Melee Group Synergy usually consists of:
- Fury Warrior (Battleshout,)
- Arms Warrior (Battleshout, Blood Frenzy)
- Feral Druid (Imp LotP)
- Shaman (Windfury, Strength of Earth, Heroism)
- Ret Pally (Imp Sanctity+Judgements; Crusader, Wisdom, Light)
- BM Hunter (Ferocious Inspiration)
- MM Hunter (True Shot)
- Rogue (Hit stuff)
Caster Group Synergy usually consists of:
- Elemental Shaman (Wrath of Air, Wrath, Mana Spring, Heroism)
- Shadow Priest (Duh!)
- Moonkin (Moonkin Aura)
- Mage (pew pew more)
- Warlock (pew pew more)
- BM Hunter (Ferocious Inspiration)
Healer Group Synergy usually consists of:
- Resto Shaman (Mana Tide, Wrath of Air)
- Shadow Priest (once again Duh!)
- Moonkin (Moonkin Aura)
- Priest, Pally, Druid (heal stuff)
Tank Synergy usually consists of:
- Main Tank (duh)
- Off Tank Warrior (Commanding Shout, Battle Shout)
- Off tank Feral (Imp LotP)
- Warlock (Blood Pact)
- Tree Druid (Tree of Life)
- Shaman (Windfury, Strength of Earth, Grace of Air, Heroism, Wrath of Air)
- Paladin (Devotion Aura, Draenei Heroic Presence; 1%+hit)
- BM Hunter (Ferocious Inspiration)
- MM Hunter (True Shot Aura)
As you can see there are alot of ways to use your raid members to provide group synergy. Some class/specs are pretty interchangeable as to where you can put them to provide group synergy.
The BM Hunter for example will provide some DPS/TPS boost to any melee or caster group you put them in. As long as you aren't sticking them in the healer group you are getting a little more out of them being there.
Shaman's are pretty good in all parties, they have the ability to buff melee, casters, tanks, and healers alike. Using a resto shaman in the tank party may give up easy access to a manatide, but it does create an increasingly higher threat ceiling for your dps to work with. Add in Grace of Air for fights that need more avoidance and personally, I'd much rather have a Shaman in the tank group than a Paladin any day. The same goes for having a resto shaman in the melee group. Just assign someone in the raid to group swap to the healers for mana tide and you are good to go if you don't have the luxury of a full time enhancement shaman.
Moonkin fall into this category as well. In most raids the caster dps synergy group tends to look like (Shaman, Spriest, Mage, Mage, Warlock). So where do you put your moonkin? Put him in the party full of your paladin healers. Increased spell crit = much larger pally heals, and increased inspiration and ancestral fortitude procs from your priests and shamans. This is not a bad thing.
I did not touch on the out of group aspects of raid synergy. Things like Survival Hunters, the extended benefits of Blood Frenzy, Shadow Embrace, Curse of Recklessness, Screech, etc. Nor did I talk about battle rez or soul stones or profession based synergistics such as drum usage.
As a raid leader and main tank for my guild, group synergy is a very interesting discussion, and the more I talk about it the more I think things out in minute detail. At first I tried to create a tank party that was built to keep me alive. The old school; Warlock, Paladin, Tree, OT, MT; type of grouping worked well until we got to Hyjal and BT. The only time now that I put a paladin in the tank group is for Fire Aura or when an Imp is just plain not an option (RoS, Archimonde). The only fight in which I have a Tree in the tank party is for Teron (and thats mostly cause there's usually nothing better to put in there). All other encounters its a shaman, a lock, and some other TPS booster (Feral, BM Hunter). This is all based on the fact that I am a warrior and not draenei of course. The group setup doesn't change much if your MT is a feral or a tankadin. The Shaman and the Imp help both non warrior tanks. Grace of Air is a boon to Bears and Wrath of Air can help keep threat high with a tankadin.
In the end, the type of synergy you wish to have is up to you. Its important to maximize what you got, but there will always be that 5th party that is an amalgamation of whats "left over". Try and give them a little too, and when it doubt the BM Hunters fit just about anywhere. ^^