| Year | Award | Category | Work | Result | Refs. |
| 2000 | St. Louis International Film Festival | Emerging Actor Award | N/A | Won | |
| 2003 | Boston Society of Film Critics Awards | Best Supporting Actor | Shattered Glass | Won | |
| Village Voice Film Poll | Best Supporting Actor | Nominated | |
| Southeastern Film Critics Association Awards | Best Supporting Actor | Nominated | |
| Seattle Film Critics Awards | Best Supporting Actor | Nominated | |
| San Francisco Film Critics Circle | Best Supporting Actor | Won | |
| Toronto Film Critics Association Awards | Best Supporting Performance – Male | Won | |
| Washington D.C. Area Film Critics Association | Best Supporting Actor | Nominated | |
| 2004 | Independent Spirit Awards | Best Supporting Male | Nominated | |
| Dallas–Fort Worth Film Critics Association | Best Supporting Actor | Nominated | |
| Central Ohio Film Critics Association | Best Supporting Actor | Nominated | |
| Kansas City Film Critics Circle Awards | Best Supporting Actor | Won | |
| Chlotrudis Awards | Best Supporting Actor | Won | |
| Chicago Film Critics Association Awards | Best Supporting Actor | Nominated | |
| Las Palmas Film Festival | Best Actor | Won | |
| National Society of Film Critics Awards | Best Supporting Actor | Won | |
| Online Film Critics Society Awards | Best Supporting Actor | Won | |
| Online Film & Television Association | Best Supporting Actor | Nominated | |
| Golden Globe Awards | Best Supporting Actor – Motion Picture | Nominated | |
| International Cinephile Society | Best Supporting Actor | 2nd place | |
| Stockholm International Film Festival | Best Actor | Garden State | Won | |
| Golden Schmoes Awards | Best Supporting Actor of the Year | Nominated | |
| Satellite Awards | Best Actor in a Supporting Role – Drama | Kinsey | Nominated | |
| 2005 | Critics' Choice Awards | Best Supporting Actor | Nominated | |
| Dallas–Fort Worth Film Critics Association | Best Supporting Actor | Nominated | |
| Glitter Awards | Best Supporting Actor | Won | |
| Independent Spirit Awards | Best Supporting Male | Nominated | |
| Online Film Critics Society Awards | Best Supporting Actor | Nominated | |
| Chlotrudis Awards | Best Supporting Actor | Nominated | |
| Online Film & Television Association | Best Supporting Actor | Nominated | |
| Satellite Awards | Best Actor in a Supporting Role | Garden State | Nominated | |
| Best Actor in a Supporting Role – Drama | Jarhead | Nominated | |
| Washington D.C. Area Film Critics Association | Best Supporting Actor | Nominated | |
| Women's Image Network Awards | Actor in Film | Flightplan | Nominated | |
| 2009 | Alliance of Women Film Journalists | Best Depiction of Nudity, Sexuality, or Seduction (shared with Carey Mulligan) | An Education | Won | |
| 2010 | Screen Actors Guild Awards | Outstanding Cast in a Motion Picture | Nominated | |
| Santa Barbara International Film Festival | Cinema Vanguard Award | Won | |
| 2013 | Satellite Awards | Best Supporting Actor – Television | The Killing | Nominated | |
| 2014 | Critics' Choice Television Awards | Best Supporting Actor – Drama Series | Nominated | |
| Gold Derby Awards | Best Supporting Actor – Drama | Nominated | |
| Ensemble Cast | Blue Jasmine | Nominated | |
| 2015 | Gotham Awards | Best Actor | Experimenter | Nominated | |
| Village Voice Film Poll | 4th place | |
| 2019 | Critics' Choice Television Awards | Best Supporting Actor – Limited Series | The Looming Tower | Nominated | |
| 2021 | Primetime Emmy Awards | Outstanding Supporting Actor in a Limited or Anthology Series or Movie | Dopesick | Nominated | |
| 2023 | Venice International Film Festival | Volpi Cup for Best Actor | Memory | Won | |
| 2025 | Karlovy Vary International Film Festival | Festival President's Award | Honoured | |
| Primetime Emmy Awards | Outstanding Supporting Actor in a Limited or Anthology Series or Movie | Presumed Innocent | Nominated | |
| (Source:) | |