How to find a player's redstone clock (or other aggressive circuitry)?

If you have access to the world file you can use a map editor/viewer to get a view of the map, and then do a filter just for redstone, overlay the second image and you will know where all the redstone is, it shouldn't take long to find the clock.

If you don't have access to the world files or the server configuration, use a custom texture pack that makes all blocks except for the ones likely to be in the mechanism (e.g. redstone) semi-transparent. Then, it's a matter of walking around until you see it: even if it's underground.

You could do it fairly quickly by editing terrain.png in your own custom texture pack, but there are several texture packs that do the same thing (like, for example, Strongestcraft).

I can't believe no one commented on Opis, by Professor Moebius: http://www.minecraftforum.net/topic/2104497-164server-admin-opis-112-alpha-now-with-entity-support/

This is a server side Forge (and client side for the admins) mod, and if you have option to use it (turn a vanilla server into a Forge one, or a Bukkit server into a MCPC Plus one), this is THE solution to this problem.

Opis is a Forge mod that allows to profile how much time is spent in each mod, chunk, even mob in the server. It shows the info as overlays over a modified open source minimap mod, and allows for tricks like teleport the admin to the close vicinity of a block or creature causing trouble, mark with a red transparent block the conflicting block, see what Forge mod causes the worst trouble... It works with vanilla or Forge modded blocks, so it can find poorly designed redstone clocks or hopper chains in a heartbeat anywhere in a server.

Direwolf20, a famous youtuber known for modded let's plays and mod reviews, made a video showing this mod:

I can't say I know of any mod to do that, though I can suggest an alternative solution. Tell him that you had suspicions and that you found it. Tell him that either he downsizes it or that you'll destroy it completely. He doesn't have to know you don't know where it is.

It's a bit of a bluff, but he'd have no reason to assume you wouldn't know where it is so it's a win-win situation. If he says he'd downsize it and nothing changes, just ban him.

Move your server file into your single player and change the skin for all common solid block (dirt,stone,sand,sandstone) to be air and then you should be able to see the circuit underground.

I would just Xray using the Nodus Xray (you can add custom blocks to show and to not show) easy finding does work if you remove ALL blocks that Orefuscator turns things into, using -xray del [ID]

If the the redstone clock has a lot of redstone torches, use zombe's modpack's cheat function, which allows you to see through blocks. After installing the mod, copy this file to {minecraft folder}/mods/zombe. After you have done this, connect to the server and press Y and then O. This will show you all the redstone Torches(on/off). If you want to see through everything (etc. blocks), press and K (default is I, but I changed it for accessibility)

Note: The config file has colours set for different (redstone) items. Light red for redstone torch(on) and dark red for redstone torch(off).

If you don't have any redstone circuits that you value, use WorldEdit, and do this commands:

//hpos1 (at a location)
//hpos2 (at another far location diagonal from the original position)
//expand vert (Expands vertically 512 blocks)
//replace 55 0

Hopefully, you will be able to find and remove the redstone circuit (the wires). If not, try it at another location.

Since you are running Bukkit you may also want to restrict redstone by using WorldGuard, and prevent lower-ranked users from placing and making such circuits.