Option 1: Eliminate the Unnecessary Rolls
While this option might take away some of the "fun of chance" of the game, for characters which simply command too many creatures, such as a cleric with a host of skeletons, this option reduces their actions to outputs based on their aggregate abilities and attempts.
Take the attack bonus of, for example, the skeletons and make that attack bonus an average, unless the attack bonus is already numerically consistent across the creatures. In this case, let us assume that attack bonus averages out to +4. Now repeat this process for damage - though if all the skeletons are medium and they all wield similar weapons or all utilize their slam attack, this step might be extraneous.
When the skeletons are fighting, use that averaged attack bonus to see how often they might hit that enemy. In this example, let us suppose that the opponent is just one human with 14 Dexterity wearing Full Plate armor - a total AC of 20.
The skeletons, with their averaged +4, would need to roll a 16 or higher to hit - this being a 25% chance to hit. Assuming the skeletons can fully surround the poor human, there would be 8 skeletons with a 25% hit chance attacking that one human. So, as DM, just decree that 2 of the 8 skeletons hit, and have them apply their weapon damage (which, again, could also be averaged if you so choose). In a larger battle with more targets, repeat this procedure as needed and move on to the Player Characters' turns.
This "diceless" method can be turned on and off between encounters with generally little effect on the outcome of battles, though it does obviously preclude the possibility of the skeletons having a very lucky or unlucky encounter.
[This option also works when the encounter might be a whole tribe of kobolds and the DM does not wish to slow the game down with such a tremendous number of rolls.]
Option 2: Meet the Horde
If the party develops a reputation for utilizing cohorts, summons, or reanimations, then it follows that their enemies would seek out to respond in kind. This could manifest either as the enemy of the party copying their tactics or countering them, though the effect would likely still be the same.
In the case of enemies beginning to adopt the party's tactics, it could be that the encounter isolates the PC's cleric's skeletons so that they must fight against the enemy party's cleric's skeletons - the DM could have easily rolled out whose groups of skeletons ekes out a win, but it would almost certainly result in a drastic reduction of the number of skeletons, and you could narrate this portion of combat relatively quickly. An example of this might be a combat which takes places in a theater - the skeletons/cohorts/summons are fighting on the stage and near the aisles - whilst the party and their enemies fight in the mezzanine. Whosoever's minions win will storm through the seating areas and up to the mezzanine, potentially cutting off escape routes.
The other method in which the enemy might deal with a party that is minion happy is to begin seeking out easy methods of attacks which do damage in an area or disable creatures in an area. Between wands of fireball, Necklaces of Fireballs, and hiring or recruiting the services of a wizard or sorcerer to utilize grease, burning hands, lightning bolt, and so on, the enemies of the PCs should have little trouble isolating and killing a good number of the minions.
Either aspect of this method require that the enemy set up ambushes, lure the PCs to specific locations, and be able to adequately gain and spread information about the party.
Of course, such a method also runs the risk of making the world appear to be in an arms race against minions - be careful in how this option is presented, otherwise the players might start to feel like the DM is "punishing" their choices. I've noticed it works best when the PCs have a "flag" of an enemy (that is, "The Miller Street Gang," or "The Army of Hatton Rand," or "The Assassins of the Genoharadan," - some kind of organized enemy), because if the entire world starts using area-of-effect attacks, the players are quick to notice that the tiniest hamlet now has a Sorcerer 4 for their leader...
Option 3: Combine Minions
Instead of the druid summoning 5 snakes with a poison effect, have her summon two snakes who have more HP, higher attack bonuses, and a poison effect that is harder to resist and does more damage. Rather than 32 skeletons, make them into 5 skeletons with better statistics.
This method would require a great deal of DM discretion, as allowing the druid to turn five snakes into one snake with five times the attack, HP, and so on is certainly not balanced. However, many players smartly recognize that combining minions almost always reduces the impact of why they wanted minions in the first place: they don't want a few, powerful things. They specifically wanted to have the battlefield control, or endless trap-fodder, or the physical safety offered by being swarmed by bodyguards.
That said, this option does become more attractive to players as they gain levels and their opponents begin to be able to simply ignore the minions and summons out of sheer vital superiority.
Option 4: Not an Option
Tell the players that while casting an occasional summon or commanding a small amount of undead will be allowed here or there, that "Diplomancy," Leadership, mass summoning, and skeleton hording are all not acceptable behavior for the setting or campaign.
This is certainly a restrictive option, but it is a valid one - I offer it with no endorsement but that it is an option, and that one of the DM's primary functions is to insure the game is timely - D&D being a tediously slow game, even under ideal conditions.