Here's a few for your reading pleasure. Hopefully a few of them are new to you. All of them are gen and involve Tony getting knocked around or suffering angst. I'll look up some more later and toss them up

Prisoner's Cinema Tony is kidnapped during a case
Half Empty, Half Full by yum@ after a bad case Tony gets everyone some coffee

Resolutions by mamapranayma : The new year is a time for change, personal growth and resolutions. For Tony however, a dangerous obsession may make this the last new year he will see. Set after 'False Witness'

Situations Tony!Whump. Tony and Fornell locked in a basement

You Wouldn't Waste The Coffee Tissue warning

So Far In Blood That Sin Will Pluck On Sin All things considered, DiNozzo had held it together better than anyone could have expected under the circumstances. (Emotional hurt and angst)

Dirtbag Remember tony's stream of chatter while chasing suspects in Baltimore? Written long before that but just as hilarious.

His Mouth Tony really should watch what he says

Moby Dick What if Frank's had hit Tony harder?

Thanks, I appreciate it! Looking forward to other recs if you have them as well.

Not sure if these fit your bill, but most of my faves are multi-chapter :)

Bone of My Bone, by Princess Fi (multiple *short* chapters, not novel length:)
http://www.fanfiction.net/s/5974346/1/Bone_of_My_Bone

Come Take Me Home
http://www.fanfiction.net/s/4605373/1/Come_Take_Me_Home

Right Place, Wrong Time, by Vanessa Sgroi
http://www.fanfiction.net/s/5014136/1/Right_Place_Wrong_Time

Moments and Fragments, by Zan65 (a series of one-shots, most of them h/c in nature, and a lot of them were later developed into full-fledged stories, so if you decide you like one, just check the author's profile to see if it was expanded)
http://www.fanfiction.net/s/4501436/1/Moments_Fragments

North by Northeast, by mamapranayama
http://www.fanfiction.net/s/4897902/1/North_By_Northeast

Hard Lessons, by Sapphyre Blu
http://www.fanfiction.net/s/5332530/1/Hard_Lessons

No Big Deal, by Mulderette
http://www.fanfiction.net/s/6423059/1/No_Big_Deal

"Missing" and "Buster", bu Mulderette
http://www.fanfiction.net/s/5890602/1/Missing
http://www.fanfiction.net/s/5996427/1/Buster

Thank you! I'll check these out. If you have other recs, multi-chap is ok, just trying to stay away from novel-length.

http://archiveofourown.org/works/10586
Unintentional Conversations by Waldo

Published:2009-10-08
Words:1807
Chapters:1/1
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http://www.ncisfiction.com/story.php?stid=04209
Boats by Xanthe

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http://www.fanfiction.net/s/6128031/1/A_glass_of_chardonnay

A glass of chardonnay by Richefic

Rated: T - English - Hurt/Comfort/Angst - Leroy Jethro Gibbs & Tony D. - Updated: 07-14-10 - Published: 07-10-10 - Complete - id:6128031
-------------------

http://www.squidge.org/ncis/story.php?stid=00810
http://community.livejournal.com/gibbs_dinozzo/138639.html
The Replacement By LushBaby

Category: Slash >> Gibbs/DiNozzo
Pairing: Gibbs/DiNozzo
Rating: PG-13
Genre: Romance, Angst
Added: 29/11/2005
Summary: When everything starts to go wrong for Tony, he fears that Gibbs is finally going to see his shortcomings. Slightly AU since Kate’s alive.
Status: This story is completed.
----------------------------
http://users.livejournal.com/_thelostcity/13643.html
NCIS fic: The Last Word, Gibbs/DiNozzo (gen or slash, you pick)

Genre: Whatever you want (slash, pre-slash, gen)
Characters: Gibbs, DiNozzo, McGee, Ziva
Pairing: None or implied Gibbs/DiNozzo
Categories: angst, anger, Tony!whump (kind of), Gibbs!whump (sort of)
Rating: PG

-----------------------
http://www.squidge.org/ncis/story.php?stid=02666

One rant, One revelation by NavyVegas

Category: Slash >> Gibbs/DiNozzo
Pairing: Gibbs/DiNozzo
Characters: Anthony DiNozzo, Abby Sciuto, Kate Todd, Leroy Jethro Gibbs
Rating: PG
Genre: Angst, Episode Related, Drama, Pre-slash
Spoilers: One Shot, One Kill
Added: 23/03/2007
Summary: Tony is less than happy after the events in One Shot, One Kill
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http://ncisfic.com/viewstory.php?storyid=72

Velvet Touch by: Nix

Rating: YTEEN
Character(s): Jethro Gibbs, Tony DiNozzo
Category(ies): Angst/Drama, Episode Related, Unresolved Sexual Tension
Pairing(s): Gibbs/DiNozzo
Episode(s): 3-04 Silver War
Summary: Silver War post-ep. Tony is neither blind nor stupid.
-----------------------
http://www.ncisfiction.com/story.php?stid=00382

Identity by rebecca

Category: Slash >> Gibbs/DiNozzo
Pairing: Gibbs/DiNozzo
Rating: PG-13
Genre: Angst
Added: 26/06/2005
Summary: Who are you?
---------------------

http://www.squidge.org/ncis/story.php?stid=00343

Keeping Watch by rebecca
Category Slash >> Gibbs/DiNozzo
Pairing Gibbs/DiNozzo
Rating G
Genre Pre-slash, Angst
Spoilers SWAK
Added 05/06/2005
Summary What the hell am I going to do with you now?
Author's notes For everyone who asked when I was going to write a SWAK tag...
Status: This story is completed.

------------------------
http://www.fanfiction.net/s/3882746/1/Taking_Turns
Taking Turns by DeniseV

Fiction Rated: K - English - Hurt/Comfort/Friendship - L.J. Gibbs & Tony D. - Published: 11-09-07 - Updated: 11-09-07 - Complete - id:3882746

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http://www.squidge.org/~peja/cgi-bin/viewstory.php?sid=44696&warning=FRT

Summary: Tony is in danger and Gibbs is his lifeline.

Categories: N.C.I.S, Television
Characters: Anthony Dinozzo, Leroy Jethro Gibbs
Genres: General
Chapters: 1
Completed: Yes
Word count: 1325
--------------------------
http://www.thetenthmuse1.madbrilliant.com/ncis/standalones/standalones_main.html

Falsely Accused: Tony meets up with the detectives of New York's SVU squad the hard way. R warnings: mentions of rape, bad language, f/f and m/m interaction.
---------------------
http://users.livejournal.com/_thelostcity/16938.html
Title: Five Times Tony Came Back From Being Undercover (Plus One)
Author: _thelostcity
Fandom: NCIS
Genre: Pre-slash
Characters: Gibbs, DiNozzo, Abby makes a brief appearance
Categories: hurt/comfort, minor angst
Rating: PG

companion piece -

http://users.livejournal.com/_thelostcity/13378.html
Title: Not Your Style
Author: _thelostcity
Fandom: NCIS
Genre: Pre-slash
Pairing: Gibbs/DiNozzo
Categories: mild angst, hurt/comfort, a bit of insecure!Tony and protective!Gibbs
Rating: PG (swearing)

http://www.fanfiction.net/s/4848216/1/Home_Truths

Home Truths by PrincessFi
Rated: T - English - Family/Drama - Tony D. - Published: 02-08-09 - Complete - id:4848216
--------------------------

http://www.squidge.org/ncis/story.php?stid=03961
http://ncisfic.com/viewstory.php?storyid=1066
Guardian by SilverFoxFiles

Category: Slash, Slash >> Gibbs/DiNozzo
Pairing: Gibbs/DiNozzo
Characters: Anthony DiNozzo, Leroy Jethro Gibbs
Rating: R
Genre: Angst, Drama, Hurt/Comfort, Pre-slash
--------------------
http://ncisfic.com/viewstory.php?storyid=401
Gunshy by: Dana Woods

http://archiveofourown.org/works/64276
Gunshy by idyll
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http://brothersinarmsfiction.com/annie/anniencis.html

Rule 13 By AnnieB

Written for Anna’s challenge on the NCISFF list. Prompt words – Snow, Fire, Holiday.
Rated PG
Mention of slash relationship.
Gibbs/DiNozzo.
Word Count: 1,055
------------------------

http://www.fanfiction.net/s/6105226/1/So_Theyll_Know#

So They'll Know by JadeBear77

Rated: M - English - Hurt/Comfort - Tony D. & Leroy Jethro Gibbs - Published: 07-02-10 - id:6105226
--------------------

http://www.fanfiction.net/s/5352813/1/The_Final_Blow

The Final Blow by Fantasygirl721

Rated: K+ - English - Angst/Friendship - Tony D. & Ducky M. - Published: 09-03-09 - Complete - id:5352813
Disclaimer: Never claimed that I owned it.

Summary: After the events of Kill Ari Part 2, Tony is plagued with dark thoughts and long hidden fears. One-shot Tony/Ducky friendship, Tony/Gibbs Father/Son.
----------------------

http://derrumtreiber.livejournal.com/11044.html

20 September 2009 @ 01:54 am
NCISFic: Tried and True
Rating: PG-13 for some swearing
Pairing: Gibbs/DiNozzo, mentions of Tony/Jeanne
Summary: Hurt/Comfort, Tony breaks down after Jeanne's accusation. Set season 5, after Internal Affairs.
Word Count: 1832
-------------------------
http://www.squidge.org/~peja/cgi-bin/viewstory.php?sid=50073
Defiance by Kate of Kintail
Fandoms: N.C.I.S
Characters: Anthony Dinozzo
Genres: General, Slash
Challenges: NCIS - DiNozzo - defy

Chapters: 1
Completed: Yes
Word count: 980
---------------------------
http://community.livejournal.com/ncis_ficathon/21860.html#cutid1
2007-08-15

Fic: All That Was Missing
Author: kuyashinaki
Written for: wondersheep
Archive: yes, please ask though
Rating: PG-13 ... at least I'd say so
Warnings/Spoilers: none
Genre: Slash, established relationship
Pairings: Gibbs/DiNozzo
Word Count: ~ 4.400
Prompt: Gibbs finally finishes the boat, and Tony's there. What's Tony's reaction? Can be gen or slash.
Summary: Tony remembers something Jethro once said. Jethro doesn't. But it's all about the boat, their relationship and Tony's insecurities.
-------------------------
http://www.ncisfiction.com/story.php?stid=03499

Purgatory by ksl

Category: Gen
Characters: Leroy Jethro Gibbs
Rating: G
Genre: Episode Related
Spoilers: Judgment Day
Added 25/05/2008
Summary: Between Judgment Day and Pardise is Purgatory. This is the conversation I wish Gibbs and Tony would have between the end of this season and the start of the next one.
Status: This story is completed.

Thanks!

Hey! I have this themed list of disability fiction, and there is a lot of h/c on there-some are quite long, and most are permanent problems, but you might consider taking a look; there will probably be some that fit your needs! Also, someone may have mentioned these, but many fics by richefic would fit your search, and I especially love In the Dark by Alkaline Teegan...Tony has migraines and Gibbs and sometimes the other teammates take care of him.

Thank you! In The Dark is actually what made me want to get recs for this theme... good taste ;)

Ah! Great minds think alike! :D it's such a great fic, though-I go back and re-read it fairly often!

"An Embarrassing Injury." I wrote this story several months ago. It seems to fit your criteria.
Summary: When Tony receives an embarrassing injury while McGee and Ziva should be listening, how funny is it really? Alternate ending to "Dead Air". G,D Father/son. A little Ziva, McGee bashing, don't like, don't read.

http://www.fanfiction.net/s/6630157/1/An_Embarrassing_Injury

Thank you! I like Ziva and McGee, but quite frankly they deserve a little bashing after that episode :p

All of my stories are GEN and include paternal Gibbs and whumped Tony. Behind the Mask doesn't have too much plot and is a tag to Missing.

http://www.fanfiction.net/s/3113195/1/Behind_the_Mask

Bad news - I've read them all. Good news - I absolutely love your stories, so re-reading will not be painful ;) Thanks!!