Fantrax is the best for leagues with farm systems in my opinion. But a secondary site like ProBoards should be used for trade talks and other things like that.
Fantrax doesn't look pretty but it works perfectly. I prefer functionality over appearance. And Fantrax has improved every year, so that's one thing I also like.
I'm not sure how much it costs but I suggest paying for the premium package at Fantrax, it's definitely worth it. If you need a player added to the database, just request it and they'll add it within 24 hours. Requesting new player positions is also possible but you need to provide proof of that, so it can't be misused. And the Commissioner has lots of options to modify the league.
Figured I'd chime in here.
I'm in 3 keeper/dynasty leagues this year, one on ESPN, one on Yahoo where we use Proboards to track farm teams and another on Fantrax. I've also previously used CBS for a minute but not enough to really provide an opinion so I'll leave them out.
I will start by saying that for any league with a farm system, Fantrax is the way to go and it's not even close. I've been in 2 leagues now where we had farm teams and used Yahoo as our main provider plus a secondary site like Proboards to track minor league rosters and draft picks. In both cases the tracking aspect slowly became a disaster. GMs regularly forgot to update their farm rosters when they added/dropped a player or called him up/sent him down; teams often picked up players in Yahoo who were on other teams' prospect rosters; messaging between GMs could be confusing (some message through Proboards, others Yahoo) and some GMs basically stopped using, checking or updating Proboards altogether. All in all, using two sites to track one league just makes for a very clunky, disconnected experience overall and you can basically guarantee that rosters will become out of date across platforms in 98% of leagues that use this format. Also, it's a ton of extra work for the commissioner to stay on top of things - I personally wouldn't ever want to run a league that uses this format.
Fantrax, while not the prettiest looking site, definitely offers the most customizability and functionality. As others have mentioned, their customer service is also great and fast. I've found that with providers like Yahoo and ESPN, even without farm teams, the lack of customizability requires leagues to have separate thorough rulebooks and trust that everyone will abide by them. Don't get me wrong, every single league out there should have a thorough rulebook, however it's nice to know that Fantrax allows you to input most if not all of your league's rules into your league's set up so that they're automatically enforced.
For leagues that do not employ farm teams, especially free or low-fee leagues that don't want to pay to use a provider (Fantrax premium leagues cost $80 per year), my personal preference is ESPN. Yahoo is definitely a bit further along when it comes to providing stats and updates but I find their interface to be extremely cluttered and annoying to use. ESPN has by far the nicest, simplest interface of the 3 providers I've discussed in here and they tend to allow a Commissioner more flexibility, especially when updating league settings mid-season (Yahoo basically locks things down so if you mess up when you create your league, you have to live with it until the following season in some cases).
TL;DR version: Fantrax is a must for leagues with farm teams, ESPN is slightly better than Yahoo for leagues without farm teams.
16 GM Dynasty
H2H Points
Weekly Matchups w/ Starts: 12F/6D/2G
G(3), A(2), +/-(0.1), Hit(0.1), SOG(0.1), BS(0.1), PPP(1), SHP(1)
W(4), L(-2), SO(4), Sv(0.2), GA(-1)
F: A. Svechnikov, R. Thomas, N. Suzuki, Pastrnak, Boldy, J. Robertson, J. Hughes, Frost, Tolvanen, Drouin, Heinen, Gallagher, N. Ritchie, Wood, Poehling, Podkolzin
D: Makar, Fox, Dobson, Byram, Dahlin, Ferraro, Michael Stone
G Sorokin, Hart, Georgiev, DeSmith
Farm: Firkus, Kayumov, Heimosalmi, Brennan, Werner, Kvaca, Parik
We moved from yahoo to fantrax about five years ago, and have never looked back.
10 team Full Keeper Roto League
4C-4LW-4RW-6D-2G-5bench-unlimited farm.
C= eichel,horvat,malkin,kuznetsov
LW= forsberg,kreider,lee,b.tkchuch,hertle,granlund
RW= reinhart,radulov,hoffman,laine,hayes
D= doughty,ghostebehere,karlsson,jones,klefbom,dahlin ,skjei
G= price,murray,grubauer,georgiev,ullmark,samsonov
under250gp=nichushkin,tuch,mathesson,marino,pujuja rvi,hosang,terry,andersson,j.hughes,patrik,crouse, zadina,podkolzin,k.miller,nedeljkovic,kravtsov,hay ton
--G,A,P,PPP,SHP,GWG,PIMS,+/-,SOG,hits,FOW,blks-Wins,GAA,SV%,saves,SO
Fantrax is good for dynasty leagues, if that's not what you're doing I'd go for Yahoo.
Los Angeles Kings
16 Team H2H Dynasty League on Fantrax
G, A, Pt, +/-, PIM, SOG, PPP, Hit, Blk.
W, GAA, SV, SV%
12 F
6 D
2 G
3 Bench
Roster
St. Louis Blues
22 Team H2H Points Based Cap Dynasty League on Fantrax
G(1), A(1), +/-(.5), PIM(.05), SOG(,05), PPP(.5), Hit(.05), Blk(.05), FOW(.01).
W(2), GAA(-1), SV(.1), SO(3)
4 C
4 LW
4 RW
6 D
1 G
4 Bench
Roster
Fantrax and officepools! Are the best. no questions.
Yahoo, ESPN, CBS, etc cannot compare
30 team league, DYNASTY
Hartford Whalers
GO CANES
WHL (24-Team Daily H2H)
Weighted Scoring: G(1),A(1),PPP(0.5),+/-(0.25), SOG/PIM/HIT/BLK(all 0.05), FOW-C(0.01)
Braham Pietasters
C(3): Barkov, Seguin, N.Schmaltz
LW(3): Gaudreau, Pacioretty, Hinostroza
RW(3): Radulov, Mantha, Dadonov
F(3): Bailey, Thornton, Vanek
D(6): Josi, Jones, Krug, Leddy, Ellis, Miller
G(1): Bishop (Sparks)
Bench: T. Wilson (RW), Boyle (C), Pirri (C), Boyd (C)
Farm: Myers (D), Husso (G), Soderstrom (G), Petersen (G), Anderson-Dolan (C), Pilut (D), Capobianco (D), Aho (D)