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Specific spells for LA rlyeh
Contact void spectre: (conjuration 6, needs s3 to cast cost is 25s. See manual for specific stats.) I can add that he spreads insanity fast in the enemy provinces he is visiting. This in combination with stealth(+25) enables some fun strats where you sneak him into enemy armies/mage centres. Also, he has the summon +5 at start for the void gate. He can also be used as a raider with some decent gear and scripted to cast luck + twist fate + attack.
Dreams of R'lyeh: (Thaum 6, needs s4 to cast cost is 4s.) Haven't been able to play around with this much, but it seems to give an mr check, after which an assasination atempt occurs (with attack/defense/mr halfed for the target).
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Clams
Early on all water gems should be saved to be used for voice of tiamat plus the occasional voice of apsu (unless you are about to fight someone underwater then you want too summon with them). Later on if there are no immidiate threat to your position investing your water gems in clams is a nice idea. use slave mages with the nature pick and equip them with forge hammers.
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Ritual attack spells and other benefits of high astral
R'lyehs high astral combined with their easy access to astral gems makes spells like mind hunt, vengence of the dead as well as their own LA spell - Dream of R'lyeh excellent spells to target pesky enemy commanders. Note that the success of these spells are greatly improved by penetration items such as spell focus, rune smasher and the eye of the void.
Other benefits of high astral is the fast mobility. Lone mages can be quiclkly teleported to the front lines (perhaps carrying valuable gems to help in the war effort), also forts under siege can quickly be boostered by gating in armies. It is worth it to read Baalz excellent post later on where he suggest an rather unorthodox warfare technique that involves heavy use of these spells.
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Fighting on land
How to deal with pesky archers : Basically MA/LA r'lyeh will field huge armies of low protection units, i.e they die fast to massed archers. There are several good answer to this. The first answer before magic can take care of the situation is to use screens. This means that small sized group are put ahead of the larger armies, the point being that archers put to "fire closest" will only fire at them and miss the majority of the arrows.
Later on you might want to get your hand on a staff of storms (through trade) that will also shut down fliers or get access to air magic of your own (fairy queen, with equipment it can also do storm, arrow fend, fog warriors - very potent spell for your masses!). In the late game communions casting army of lead/gold will also take care of archers (and also make your lobos pretty great actually). Another answer is darkness;
Darkness: Many players new to r'lyeh doesn't realise the potential of having 100% DV on all their units (this is not true for some of the LA freespawns but darkness is great for LA anyway) and combining this with darkness. Darkness cuts your opponents attack and defence values in half and precision by 75% (both archers and opposing mages will be greatly hampered by this spell).
Other buff spells for the endgame Through communion a lot of spells are available to cast. Do not feel limited to experiment on your own but some of my favourites include army of lead/gold, antimagic, darkness and will of fates. Not only will they greatly improve your fighting, they will make fights look pretty
http://img443.imageshack.us/img443/2310/bild1gn0.jpg
http://img443.imageshack.us/img443/5774/bild2iq5.jpg
Spells to kill with This really depends on what you are up against. For the standard armies, I tend to use the starspawn that has death on them to do the fighting (should be around 50% that has death). I script them to cast nether darths, a spell they can cast almost endlessly. For tougher foes, paralyse/soul slay/enslave mind or against groups of heavy foes i tend to use starspawns with some earth and cast communion + summon earth power + gifts from heaven. What spells to use really depends on what you are up against and what spells you can cast at that point.
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Underwater fighting
Underwater fighting is not so much about offensive spells, instead the outcome tend to be heavily influenced by the quality and quantitity of troops. Specific underwater spells to aim for if you fear an attack by atlantis/oceania are school of sharks, shark attack, friendly current and water ward as well as any other buff spell you can get your hands on. Equiping your mages with water gems and spamming out some water elementals can make a difference in how well the fight ends up as well.
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More info if you are playing MA/LA rlyeh
http://www.freewebs.com/dominions2/rlyeh.html
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All ideas, feedback, question, flames or general thoughts on new sections that would make for interesting reading in this guide feel free to post them here