Canon: First series of Pixma and many earlier that use BCI 3 and/or 6 ink tanks have among the lowest TCO available, and their output is generally nice too.
HP: Most have integrated head cartridges so are very expensive over the long haul unless you refill the carts yourself (5 to 10 times is usually the limit before the heads finally give out). Usually very good output quality. Most have U-shaped paper paths which can be rough on media like labels, heavy stock, glossy photo paper that wasn't specifically designed for it. Not uncommon to jam as well. I can't recall any recent Canon jamming on me.
Epson: known to have clogging problems with the root cause being the relatively cold print head technology (piezo - most others use thermal heads). If you print a lot, clogging shouldn't be too much of a problem. Clone ink tanks are available - if you can, start with clone tanks from the very beginning. Make sure you buy tanks with ink specifically formulated for Epson because of the piezo technology noted above. Also be very quick about changing tanks. Inks for Epsons should all be pigmented and designed to be fast drying - a recipe for clogging. Output is usually very good.
I seldom mention Lexmark because output quality is usually not up to snuff and you'll take it in the shorts on ink unless you refill them yourself (integrated head carts).
Brother has a new line of AIOs that all use the same print engine and passive ink tanks (separate for each color) like the good Canons. Unfortunately can only be had as AIOs, no printer only units. The models from the MFC-420 up differ only in extra features: sheet feeder, flash card readers, etc. Best networking of any current printer family - some models have built-in wireless, all have Ethernet. I'm getting mixed reviews as to output quality. Haven't had hands-on with Brother here - but one of them will probably be my next unless Canon comes to their senses (or cloned ink tanks are out) by then. Are inexpensive to buy (the 640 is currently $125. AR at Office Depot - see my thread in Hot Deals) and should be inexpensive to run.
Shameless plug here: I use and recommend Swiftink.com ink tanks for my Canon iP3000. Not the cheapest, but output quality is excellent. They have clone tanks for most Canon, Epson, Brother; and have refilled tanks (and/or refill kits) for HP and some Lexmark.
.bh.