Sparx - I keep an eye on Ebay and have been noticing prices coming down on Hammonds...this may be a natural result of a still sluggish US economy. My advice and I hope this doesn't sound pedantic:
The A-100 series (A-101, 105, 122, etc.)tend to be much better buys on Ebay than B3 or C3s and are identical mechanically, the only difference being that they have built-in amp/speakers and reberb (which IMHO is an advantage). B3s tend to be inflated in price due to the hype and mystique around the famous players. The main thing to keep in mind buying a 50 year old piece of electronics, is no matter how 'over-designed' it was in 1950, it has probably has 50+ year old electronic and mechanical parts will definitely need replacement or maintenance (capacitors, tubes, switches, pots, transformer, and even wiring harnesses). You referred to the 'tubes' (or valves) and yes I agree with Ken replacing them will be the least of your maintenance problems since several companies in China, Russia and elsewhere still manufacture them. There are several companies that also make replacement solid state electronics for these organs (notably Trek II) which may be a more practical alternative for a church who does not want the maintenance issues with maintaining old vacuum tube electronics. Keep in mind the main 'engine' of the Hammond tonewheel organs is a spinning tone generator that requires regular oiling and maintenance. I recently started one that had not been running for approx. 15 years - after oiling and hand turning it 20 or so times it came squeeking to life however I might not have been so lucky and found it useless. Ken's comments about replacement of parts on electronic clone organs may be well taken - it is true that many of parts for Hammond A-B-C-R-M series organs will probably always be available in our lifetime (although some are not)....by contrast my Korg BX3 clone that I use for gigging has already been discontinued and I fear if I have to ever order electronic parts). Regarding the new electronic B3s the reviews are very flattering however the relative cost factor (£15,000 or us$21,000) is probably more significant consideration than the parts/service life. For a church there may be definite advantages to having program and MIDI features since you probably won't just be playing blues and jazz on it like me.
Finally the leslie is a primary component of that sound you probably crave and I agree with Ken's comment about getting a leslie. A vintage tone cabinet however may not be a waste and can be used in conjunction with a leslie. Alternatively I would consider not going 'vintage' with the leslie speaker and looking at Hammond-Suzuki's 122a,b or 3300 models which are more powerful and dependable than the original (now 50 year old) Leslies. Depending on the organ you may need an intermediate hookup part but not rare or expensive. There are other manufacturers making 'rotating speakers' including Motion Sound and Speakeasy who make improved replicas....they generally have better speakers, amps, cabinets and horn drivers than the old ones unless refurbished. Good luck....take your time since there where 100s of 1000s of these organs built so they are not on an endangered species list quite yet!
Hope this helps,