We recently bought two HiSeq 4000 instruments to run larger RNA-seq and exome projects on. Over the next few months we'll be transitioning other library types where we can, and think perhaps 65-85% of the work we do can be ported over from the 2500. Look on eBay and you can find multiple HiSeq instruments for sale, and I've been contacted by increasing numbers of people wanting to sell 2500's - but buying a 2nd hand machine is not as simple as it looks.
Be careful when making that purchase: A previous boss purchased two ABI3700's, one of these turned out to be a very expensive mistake, but the pair probably worked out cheaper than new instruments or second-hand ones from ABI. So before parting with the bargain price (!) of $388,895.22 for the V4 2500 instrument in the image above you should check who you are buying the machine from, make sure they are a reputable lab or reseller. Ask for a break down of the problems the instrument has had; have Illumina's TechSupport been working on it every week, or has it worked perfectly from install? A point to check is what Illumina will charge you to bring the instrument back under warranty. This might be the biggest expense other than the instrument and you may need to pay up to $50k for a software licence on top of that. A 2nd hand machine may work out to be much less economical than a new one in the medium term.
I'm not sure how quickly the 4000 is being adopted, but it seems to be much slower than the move from HiSeq 2000 to 2500. This is almost certainly down to the 2500 being the pinnacle of the original Solexa technology, it is very similar to the 1G we started with - but putting out 1000x the volume of data.
How much is a 2500 worth: I was surprised to see instruments going for so much on eBay and from equipment resellers. As the state of the instrument will dictate what Illumina charge to make it operational (see above) it is difficult to say for certain how much a machine will cost over-and-above the purchase price. But with perhaps a $100,000 bill op top you might be better off asking Illumina for a deal on a new 2500. If I wanted a 2500 I'd be unlikely to pay much more than $100,00-$150,00 depending on its provenance.
Do you need a 2500: The new patterned flowcell chemistry is a big step forwards, and we'd not have the X Ten without it. However a very large number of our libraries are not officially supported and that may ultimately prevent us from running everything on patterned flowcells, so in a nutshell access to 2500 looks to be important for a while to come. But the development of the 2500 appears to be shelved so while we can continue to run some of these unsupported (on HiSeq 4000), or even unsupportable, library prep types; these are going to look increasingly expensive when compared to exomes and RNA-seq on 4000 (or even X-Ten).