Yes, there is.
As of 1.4.2, /weather (operators only) can be used to control the weather server-wide.
/weather
clear/weather rain/weather thunder
You can also optionally specify the number of seconds, up to a million (that's 11 days and ~14 hours).
For example, /weather clear 60 will clear up the weather for 1 minute only.
Also, the /toggledownfall command (also ops only)
stops/starts rain or snow on a vanilla server.
It was added in a beta 1.9 pre-release.
gaming.stackexchange.com/users/9752/a cat
Bukkit has integrated the commands into it.
You need OP
but: /weather sunny <time> /weather
storm <time> /lighting
<true/false> /thunder <true/false>
gaming.stackexchange.com/users/9576/Evan Darwin
There is no such command available in vanilla Minecraft servers, sorry.
See lunboks answer for more up-to-date info.
gaming.stackexchange.com/users/8771/Andrew Lambert
On a vanilla server, you can use the command /toggledownfall to turn rain or snow (depending on what biome you are in) on and off (depending on whether or not it is currently raining/snowing)
You must be an operator in order to use this command.
It is possible to set your server so that toggling rain or snow is unable to be performed.
This setting is not altered by an in-game command, but by an owner in the server's settings, much like the server's difficulty or whether or not flying is allowed.
This command has no effect in the following biomes due to the biomes not allowing rain/snow: Desert, DesertHills, Hell, and Sky.
The Hell biome is the only Biome present in The Nether, and
the Sky biome is the only Biome present in The End.
gaming.stackexchange.com/users/30173/pizkwat
You can use /weather <sunny|rain|thunder|clear> ; I am not sure if you can make it snow or not.
You can also use /toggledownfall .
(All of this is as of 1.7.2.)
gaming.stackexchange.com/users/62483/1Melaniheart2
The latest version of Minecraft (1.5) brings, among other things, a number of different weather conditions.  Most of these annoy me to no end.  I tend to spend a lot of time playing on an SMP server, so I'm wondering if at least here, there is a way to effect changes in the weather: maybe through server commands?
Is there an SMP Server Command to change weather conditions?
gaming.stackexchange.com
<minecraft-java-edition><minecraft-commands>
gaming.stackexchange.com/questions/20746
gaming.stackexchange.com/users/3114/GnomeSlice
You can use weather clear 60 to clear up the weather for 1 minute. You can also use toggledownfall to turn rain or snow on and off. There is the ability to change weather conditions by following a set of instructions on a vanilla server, provided you are an operator.
<true/false> /thunder <true/false>
There is the ability to change weather conditions by following a set of instructions on a vanilla server.