As a villain (D&D 3.5, source = Book of Vile Darkness). It seems like it would be a fantastic "behind the scenes" villain, but it seems like even at its higher levels its abilities don't give it much oomph for direct confrontation. No spellcasting progression really cripples it, I think, but the concept is just so great for a baddie.

Since it doesn't have any casting progression, and all its abilities are fairly weak (IMO) for direct encounters, I feel like it could be put up against a group of PCs of lower level than it and they would do fine. Thoughts?

This prestige class seems like a great side quest actually. It has great out of combat abilities but this does not seem a very good combat prestige. I just noticed that you dont need to be a spell caster to be a cancer mage. The abilities seem suited to a rogue or a fighter. Fort saves. Recently opened sewers or something in a city. A rash of disease and plague have seiged the city. The cancer mage walks up to a pc looking like a particularly ugly beggar. He infects one of the pcs and the pcs have to hunt him down or have their teammate die.

Book of Vile Darkness, p. 52, actually.

Depends...

Disease Host (lvl 1) + Festering Anger (BoVD, p.30) + Vile Rigidity (BoVD, p. 32) = Arbitrarily high STR and NAT Armor.*

Aeshkrau Illumian (bonus spell slots derived of STR score). With an arbitrarily high STR score, you'll get an arbitrary number of spell slots...*

• Aeshkrau Illumian Rogue 1 / Fighter 1 / Cle 2 / Cancer Mage 1 (Cle +X / Cancer Mage +X)
  
• Aeshkrau Illumian Rogue 1 / Fighter 1 / Spirit Shaman 2 / Cancer Mage 1
  Add Versatile Spell Caster (Races of the Dragon, p. 101) and transform two of your arbitrarily high number of X level spell slot into an X+1 level spell slot. Rinse, repeat.

*Limiting it to...something could make it not so... completely broken...

That said, the Viral Ally ability could lead to interesting things... a disease that acts as dominate person...

Nitpick: BoVD is a 3.0 book.

The Cancer Mage: Oh boy. I usually love PrCs that are villainous. I have never been able to wrap my head around the Cancer Mage. Too disgusting. I may have to make an attempt at a memorable one for my Tabletop campaign.

At this time I have no advise for how to make a decent Cancer Mage.

I lump 3.0 and 3.5 into the same thing unless something was specifically axed/updated for 3.5. After all there are no written rules that say they are actually different....unless there are?

Whisper, those are great ideas. And I didn't really take into account giving it those feats from BoVD.

Yes, the Viral Ally ability is pretty nasty come to think of it, considering the victim gets no saving throw to avoid the Dominate effect (but they do get a regular Fort save vs. disease). Also, the Disease Form seems powerful now that I take a second look at it...it seems to be its own thing. It's not invisibility, it's not etherealness/incorporeality...seems when it's in Disease Form it's technically undetectable and and indestructible. I wonder how the spell Dance of the Unicorn would affect a Cancer Mage in Disease Form...

Hmmm. If DotU's CL is higher than the Cancer Mage's HD, it would negate any offensive effect of the disease form. Furthermore, I'd treat it as if Remove Disease had been cast upon the Cancer Mage.

Just have the Cancer Mage watch out for those pesky clerics casting Remove Disease on somebody he had infected through his Disease Form ability...

<<...>>

Hmmm...

The Tomb of Morbis
Hook:
The location of the ancient tomb is unknown, but rumor has it, that many treasures and and much lore has been hidden there.

Outline:
The tomb features the standard obstacles; a smattering of traps, some undead creatures, etc. The PCs work their way through it, coming to the center of the tomb, expecting a 'boss fight' - and instead, there's... nothing.

Aftermath:
They retrieve the treasures and return to town. Shortly thereafter, one of them begins to feel faintly sick, suffering cold-like symptoms.
Over the course of the next few days, a flu epidemic is sweeping through the city, originating among the poorer areas but quickly spreading.

What really happens:
Locked in the center of the tomb was indeed Morbis, a powerful cancer mage who waited in disease form, infecting on of the PCs and 'riding' it into the city.
Since remaining in a PC that just got a decent amount of treasure in his hands (and can thus easily afford having Remove Disease cast upon him) is dangerous, Morbis removed himself from the PC and began infecting city folk.

As if Morbis' release from the tomb and his running free through the city wasn't enough, Morbis is carrying an ancient disease that wiped out a forgotten civilization / race: A disease possessing innate Spell Resistance that weakens body and mind (Con & Wis damage). Only the most powerful of clerics can remove this disease - and soon find themselves asked / begged / coerced / blackmailed / forced to heal the wealthy and powerful.

Conclusion:
Can the PC find Morbis and stop him from infecting people over and over ? How do they deal with friendly NPC that suddenly hinder / attack / betray them (victims of Morbis' Viral Ally ability) ?

Whoa that adventure sounds awesome!

Ah man that sounds awesome. Question. The people dominated by the disease are they still weakened by the disease. It could be terrifying a ton of weak and nearly helpless people attempting to kill the pcs. Some literally die or fall unconscious as they attempt to attack the pcs.

Yes; the domination is an effect in addition to the disease.

The 'ton' is going to be unlikely, as each Viral Ally requires the Cancer Mage to invest it with 3 points of his intelligence, thus limiting the number of active viral allies.

As has been noted, some of the diseases the Cancer Mage has access to were not properly thought out. It'd be wise to limit the number of stacks of those diseases to the levels of Cancer Mage a character has. (People without levels in Cancer Mage are limited to one stack.)