Toner costs much more per purchase than inkjet ink, but each cartridge lasts much longer so per page they are considerably cheaper. Some cheap lasers aimed at the home market do not work out as cheap (sometimes noticeably more expensive than other lasers) per page, but will still beat a 'jet in the long run.
If you do very little printing, then the inkjet will win overall but if you do a moderate amount or more even a cheap laser will work out cheaper in the long run. But if you only do a little printing there is another noticeable factor against inkjets - they tend to gum up if left alone for a couple of weeks so you end us wasting half your ink doing head cleans next time you use it - bringing the cost per page up higher. My last Epson was terrible for this, and it wasn't a cheap grotty model either.
On good photo paper a good inkjet will produce better photo results than a cheap or mid-range laser, often better than an expensive model. But that again brings up the cost considerably, and on normal paper (standard 80gsm/90gsm stock) all but the cheapest lasers will win out these days. And if you plan to print much plain text (letters, documents) again the laser wins (you don't want to use good photo paper to get crisp text from an inkjet when you can get the same text quality on standard stock out of the laser.
There is also the problem of speed. Never trust an inkjet's claimed speed. My last one claimed "up to 20 pages/min" but it couldn't even pass blank paper through at that rate, and its highest speed setting wasn't worth bothering with. That lovely full page photo could take a number of minutes to create - my laser will kick its version out in seconds. I would doubt the pages-per-cart claims of inkjets too, especially for colour output as nth figures are based on colour text not blocks of colour like a chart or photo, much more so than lasers which in my experience get much closer to their rated output per cart.
These days I go with a colour laser, my current one is a Xerox 6125 which I got a good offer on last year (lower price and free toner carts, which brought the effective price below the cheaper units I was considering) and have been very happy with it, and if I want a few more professional quality photo prints I take the files to Boots or Tesco and use their facilities or self-serve printing machines. What I used to do was to have a B/W laser for docs/letters/draft and a colour inkjet for anything that absolutely required colour.
Don't get the cheapest colour lasers as they sometimes have noticeable banding issues in colour output and once you tot up all the consumables (check how long the drums last before needing to be replaced as well as the toner) don't work out a lot cheaper than jets. If you can get print samples of plain text and business graphic (text with relatively flat colour like charts and such) and photo output for any model you consider just to be sure. My Xerox 6125 has decidedly better photo output than my brother's Samsung 310 (though the Samsung's photo output isn't terrible, its basic colour output fine, and b/w output no worse than the Xerox).
Two other points to consider: a laser will be much quieter, but most colour lasers are significantly larger and need more space around them for ventilation.
While I would be inclined to use after market cartridges as they are much cheaper then originals, and printers are generally cheap relative to the costs of consumables, not all after market cartridges are equal and the quality is not always as good as the originals.
I believe that "Which" in the UK is a Consumer funded organization. This article talks about replacement ink cartriges, and has a useful table on the their users experiences. In summary, 63% of users had no problems, about 35% had problems related to print quality, 3% complained of ink spillage and 10% complained of other problems. (I have no idea why these figures add up to > 100% !!!). If you happen to be in the UK the article is also useful as to investigating your rights as a consumer.
A report (requires subscription) on printer reliability from the prominent Consumer Supported testing company in New Zealand found that 25% of the people they sampled had problems with generic cartridges compared with 6% of those who used same-brand cartridges.
In New Zealand we have strong protection laws, and the laws prohibit manufacturers from denying warranty claims if you use compatible consumables where the consumables were not likely the cause of the problem. You might want to look at your local laws and be guided somewhat by whether you have statutory protections.
Best Answer
Its a good idea to your homework before getting a printer - some brands are easier than others (canon has been reliable for us, tho we eventually worked out how to do it with dells too) - generally refilling the ink will void your warranty (but in many cases, that's easy to work around - swap in a non refilled cartridge if needed). There is also supposed to be some risk of print head clogging.
In my experience i haven't had too many issues with refilling printer inks. Apparently the formulation differs based on the ink type (pigment based ink vs Dye based ink) - which is why there's brand specific inks.
Dumb cartridges refill better - IE, the cartridge itself dosen't have the print head built in, and as such there's no 'intelligence' in the cartridge. Some printers also have RFID chips to monitor if a cart is genuine (dell does this. You can sort of tell the printer to ignore an empty cart and print anyway, so its an anti 3rd party ink rather than an anti refill measure. Ideally cartridges should have NO logic whatsoever in them, or minimal logic. We've never had print head clogging, so far, but in general deep cleaning should fix it (or in many cases they are user replaceable - I haven't worked out how expensive that is yet)
Not all ink carts need you to drill a hole - with canons, we punched a hole in with a special tool, and with some others (dell), you inject the ink with a hypodermic needle into one of the holes already on the printer.
Finally, most printers will NOT detect ink levels on refilled cartridges, so you'll need to monitor ink levels yourself. Its fairly easy on printers with ink tanks, as opposed to having the ink soaked in a sponge, but its something to keep in mind.
Laser printer toners.. eh, don't do it yourself. that dust is NASTY. I've seen some office printers use big bottles of toner which might be more sensible. For regular printers... its probably not practical.