Tenjho Tenge had some bowling (mostly fighting, but still...).
Shugo Chara has an episode with soccer (football) and a couple of episodes with snowboarding.
Kimagure Orange Road has episodes with tennis, pro wrestling, judo, surfing, rowing, and skiing. Possibly some swimming. There's also a 3-legged race for a school activity.
Maison Ikkoku also features characters playing tennis. There's also a baseball episode, one where they go skating, and a swimming episode all which featured the two main romantic rivals competing over the female love interest.
More tennis in
Ai Yori Aoshi: Enishi episode 3. Also features swimming (mainly ep.2).
Peach Girl features some swimming too. And I think I remember some basketball.
There's swimming in
Golden Boy. It gets kinda naughty, though. And bike racing. Sorta.
Speaking of cycling, there's
Over Drive. Although this might be sports anime.
Surfing is also shown in
5 Centimeters Per Second.
Ah My Goddess! (TV) features some rally racing (s1,ep.10), go-karting (s1,ep.17), mini-bike racing (s2,ep.11) and some BMX racing (s2,ep.14). The other incarnations (movie and ova) also feature some of this.
Episode 12 of
The Adventures of Mini Goddess features baseball. And episode 33 has fishing.
You mentioned
FLCL and baseball but could airsoft (ep.5) be counted as a sport?
Episode 9 of
Strawberry Marshmallow features baseball plus soccer. (Or was it soccer plus baseball?)
Basketball is featured in School Rumble (s2,eps.8 & 9). I also saw arm wrestling and a little bit of chess and cards (s2,ep.10). There's some pro wrestling in there somewhere too (s1,ep.20).
Gokusen features boxing.
Revolutionary Girl Utena features fencing.
Kaleido Star: New Wings features an episode (s2,ep.6 (ep.32)) where the characters compete in figure skating. Hell, the whole show is pratically sports anime anyways (acrobatics).
Then there's the figure skating anime
Ginban Kaleidoscope.
There's some gymnastics in
DNA^2.
Some of the side characters are members of the volleyball club in
Minami-ke, featured in episode 5.
The
Lucky Star OVA also has volleyball.
Manabi Straight features dodgeball in episode 3.
A dodgeball match also appears in episode 10 of
Negima!.
Does Mahjongg count as an odd or obscure sport? Well, there's
Akagi and
Saki.
In that vein I guess I should mention
Hikaru no Go, then.
Admittedly,
Suzuka is billed as a sports anime, but I think the track and field stuff is purely a
MacGuffin.
And that's not mentioning the numerous school athletic festivals featured in various anime like the aforementioned
Lucky Star and shows like
Azumanga Daioh.