I started with the Red Box back in 1980, and then went on AD&D. Then, in 1986, I started playing GURPS. By 1988, we didn't play any other system, and that stayed true until 3e. Since 3e, I have played D&D almost exclusively. My GURPS Fantasy game (which some players have asked me to bring into d20) ran for over 10 years. My GURPS Supers game ran for 8 years. My current D&D game (chronicled in our story hour) has been running for over 3 years.
Both systems have advantages and disadvantages.
First: GURPS and D&D have converged, somewhat. The first thing I thought, when I saw the 3E PHB was "
Wow...it's a lot more like GURPS, now." GURPS' biggest strength is it's customizability and flexibility. Don't like the advanced combat rules? Don't use them. Don't like magic? Don't use it. And so on. D&D 3e and 3.5e, doesn't offer as much flexibility, but it offers a much wider player-base and a greater deal of support.
Character advancement varies between the two systems. In D&D characters advance quickly, and become quite powerful at high levels; they become heroes of legend, untouchable by the threats of low levels. GURPS characters advance more laterally, growing in small increments, and while they may become extremely competent, they always will be relatively vulnerable. The range in power is much more condensed, which is a double-edged sword, as it means the PCs are never super-human, but they can also feel like they never truly advance beyond their starting design.
Combat in GURPS can be simplistic or a complicated affair. It allows for much more verisimilitude in body locations, armor factors and the like. You will find much better support for a DEX-based fighter in GURPS, where agile warriors get bonuses to their defense as well. However, GURPS can also degenerate to long series of dice rolls until someone rolls a failure (I specifically recall a rapier duel between two elven princes in my game that ran for a half-hour real-time before someone drew blood). GURPS can be made more heroic...but in the same way that D&D can be made more gritty.
Both systems have excellent support, although D&D's support base is larger and has much more material available. GURPS offers a wide diversity of world settings and many more options for compatability of different options. D&D is much more tightly focused on the fantasy genre, but has excellent support on them.
GURPS offers much better support for a wide range of archetypes, and is much less likely to force you to a particular character design. Want to create Zatoichi the blind swordsman, Frair Tuck or One-armed Jack the Rogue? GURPS makes it much easier. However, GURPS character creation is not more involved than even 3E D&D character creation, and given the system's lethality, this can be off-putting to some (and a boon to others).
Both rules systems have their flaws. The current incarnation of GURPS is over 15 years old, and many feel that it's long overdue for a revision. Both systems have their loopholes, powergamer exploits, vague rules and 'dump stats'. For every 3.5 Trip-cycle, you have a GURPS Eidetic Memory. Each system is an excellent rules set, and each can be used effectively for a variety of ends.
Which do I prefer? D&D. I loved GURPS, but in some ways, it's too mechanical for the variety of fantasy I enjoy. Despite the avowed flexibilty, many characters still end up converging on the same skills and feats, effectively creating 'pseudo-classes'. GURPS even features 'packages' to this end, which are half-feat/half-prestige class. I enjoyed GURPS combat system, but it tended to bog us down, sometimes, as combats could drag on, while in real time, only 5 seconds had passed. The detailed armor, hit-locations and other systems tended to create a great deal more bookkeeping than we enjoy, and the ROI of verisimilitude wasn't worth the perceived lack of fun required to maintain it.
Further, for a fantasy game, we often found that power-levels, relatively, didn't scale well. A competent fighter might become ultra-skilled, but a mage never truly got sincerely more powerful (or indeed, as powerful as most mages from popular fantasy and legend tend to become). Fireballs in GURPS are, for all intents and purposes, wonky arrows.
However, GURPS will serve you just as well for a Fantasy game, if that's your preference. The onus is on what the players and DM/GM enjoy, and what aspects of play are most important to them. GURPS has places where it's verisimilitude can break down as well, but it also is rather nice to know that the barbarian will always be somewhat threatened by orcs...at least orcs with bows, anyhow.
If you have some specific things that do or don't appeal to you, I might be able to tell you which system addresses them better, IMHO.